mtGenome Sequencing of NIST Reference Materials and ... · NIST Standard Reference Materials (SRMs)...

mtGenome Sequencing of NIST Reference Materials and

Population SamplesKevin Kiesler, M.S.

Research Biologist - NIST Applied Genetics GroupISHI Workshop: The Future is Now for MPS mtDNA Analysis

September 24, 2018

Outline

• Reference materials and mtDNA sequencing

• Population scale sequencing

• Informatics

First – the Disclaimer

• Disclaimer - Points of view in this document are those of the authors and do not necessarily represent the official position or policies of the U.S. Department of Commerce or the Department of Justice. Certain commercial equipment, instruments, and materials are identified in order to specify experimental procedures as completely as possible. In no case does such identification imply a recommendation or endorsement by NIST, nor does it imply that any of the materials, instruments, or equipment identified are necessarily the best available for the purpose.

• All work presented has been reviewed and approved by the NIST Human Subjects Protections Office.

What is this?

A) Time machineB) Water purifierC) Steam locomotiveD) Mass spectrometer

What is this?

The PLEX-IDFrom Abbott Molecular& Ibis BiosciencesSample plates stack here

Sample purification goes on inside here

The mass spectrometersits inside here

NIST evaluated this system in 2012 for potential “rapid, simple” mtDNA analysis

mtDNA by Mass Spectrometry

• PCR across HV1/HV2/HV3• Eight tri-plex reactions = 24 amplicons

mtDNA by Mass Spec

• Desalt PCR products (automated)• Electrospray injected Time-of-Flight (ESI-TOF) mass spectrometer

• Review data for “trouble”• Sodium adducts, overlapping peaks, etc.

• Compare to database• Known mtDNA types• Masses of PCR products

• Predict DNA sequence• Paper: compared with Sanger

• n = 711 samples• 99.97 % concordant

Outcome: Simplified, faster workflowAlmost as informative as Sanger

NIST Standard Reference Materials (SRMs)

• ISO/Guide 30:2015• Reference materials (RMs) and certified reference materials (CRMs) (defined in 2.1 and 2.2)

are widely used for the calibration of measuring apparatus, for the evaluation of measurement procedures and for the internal or external quality control of measurementsand laboratories.

• Assess a new technology - calibration• Evaluate a method - implementation

NIST Mitochondrial Sequencing SRMs

• SRM 2392• Three components

• Component A: DNA from cell line CHR• Component B: DNA from cell line 9947A• Component C: Cloned fragment from HV1 region of CHR containing C-stretch

• SRM 2392-I• One component

• DNA from cell line HL60

• Characterized with Sanger methods• Released in 2001

Assessing NGS Using Reference Materials

• In 2012, all we had was a SOLiD system…• Sequencing by Oligonucleotide Ligation and Detection (SOLiD)

• Ligation chemistry based (it’s complicated) system for whole human genomes

• Very high coverage mtGenome sequence• ~ 45,000 X

https://www.slideshare.net/PaoloDametto/new-generation-sequencing-technologies

All the Sanger-Based Information Checked Out

√√√√XXX√√

√√√√√√√√√√√√

There was no software available thatcorrectly handled these C-stretchinsertions with forensic nomenclature.

Reference material

Technology

We Could Detect Some New Features!

• Heteroplasmy below what we can see with Sanger methods

SRM 2392 Component A (CHR)Position 1,393 R (17 % A)

SRM 2392-I (HL-60)Position 2,445 Y (7 % C)

We Sent Some Samples to Service Labs, Friends

• Beckman Genomics sequencing service• Seven mtGenomes One lane on a HiSeq

• ≈ 40,000 X coverage!!! (≈ 3 to 4 million bases each)• Too much to display in IGV (not enough RAM)

• Edge Bioserv (Gaithersburg, MD)• Ion Torrent Personal Genome Machine (PGM) in 2013

• Seven mtGenomes on a 314 chip• ≈ 200 X to 400 X coverage

• Illumina MiSeq in 2013• Seven mtGenomes on 2 x 150 v2 chemistry• ≈ 10,000 X to 20,000 X coverage

• Children’s National Hospital (in collaboration)• Pacific Biosystems RS in 2014

• Long-read technology, low coverage• Some variants missed

Then We Got Some Desktop Sequencers of Our Own• Ion Torrent PGM

• September 2012• Chemistry improvements over time

• 200 bp, 300 bp, 400 bp, HiQ

• Illumina MiSeq• September 2013• Chemistry improvements over time

• V2 2x150 bp, V2 2x250 bp, V3 2x300 bp

Multiple Orthogonal Measurements

• Great approach for certifying reference materials!

SRM 2392Component

A Component B SRM 2392-INucleotide 64 T 1393 A 7861 C 2445 5149PGM Edge 26.8 21.2 72.7 10.6 5.1PGM NIST 1 24.3 15.6 45.0 7.5 9.1PGM NIST 2 25.0 17.5 65.7 7.7 7.7PGM NIST 3 29.7 16.5 59.4 7.7 7.7PGM NIST HiQ 33.2 15.2 77.7 7.7 8.4MiSeq Edge 33.0 19.0 87.4 10.7 6.8MiSeq NIST 31.6 17.9 88.4 9.1 6.4HiSeq BC 30.6 16.9 88.3 7.4 7.1SOLiD NIST 29.0 16.7 87.3 7.3 7.0Average 29.2 17.4 74.6 8.4 7.3St. Dev. 3.1 1.7 14.5 1.3 1.1


• Great approach for characterizing reference materials!

SRM 2392Component

A Component B SRM 2392-INucleotide 64 T 1393 A 7861 C 2445 5149PGM Edge 26.8 21.2 72.7 10.6 5.1PGM NIST 1 24.3 15.6 45.0 7.5 9.1PGM NIST 2 25.0 17.5 65.7 7.7 7.7PGM NIST 3 29.7 16.5 59.4 7.7 7.7PGM NIST HiQ 33.2 15.2 77.7 7.7 8.4MiSeq Edge 33.0 19.0 87.4 10.7 6.8MiSeq NIST 31.6 17.9 88.4 9.1 6.4HiSeq BC 30.6 16.9 88.3 7.4 7.1SOLiD NIST 29.0 16.7 87.3 7.3 7.0Average 29.2 17.4 74.6 8.4 7.3St. Dev. 3.1 1.7 14.5 1.3 1.1

87 %

It can also educate you about your technology.


• Great approach for characterizing reference materials! SOFTWARE

Conclusions

• Reference materials • Can identify technical limitations/bias

• Often need multiple measurements• Orthogonal techniques

• Help to select best procedures

Population Scale Sequencing

Project Planning - Goals

• Submit forensic-quality whole mtGenome data to EMPOP• Current database (V3, Release 11)

• n = 26,127 control region sequences• n = 256 whole genome sequences

• NIST population samples (n > 1,000)• African American, Asian, Caucasian, Hispanic

• Sequencing plan• Start with Caucasian population• ≈ 440 mtGenomes

Project Planning

• Questions• What instrument do we use?• What protocol/chemistry do we use?• What analysis procedure do we use?

• Software, data review, etc.

Ion Torrent S5 Ion Chef

Illumina MiSeq FGx

Project Planning: Instrument Selection

• Considerations• Cost• Time/labor

• Automation

$-

$5,000

$10,000

$15,000

$20,000

$25,000

$30,000

S5XL AutomatedLibrary Prep

S5XL ManualLibrary Prep

MiSeq ILMNMethod

MiSeq AFDILMethod

Cost Per 96 Samples (Approximate)

Project Planning: Protocol Selection

• Options• Illumina whole genome procedure

• Long PCR primers developed by Dr. Mark Wilson’s lab• TaKaRa LA Taq• Illumina Nextera XT library preparation• Illumina MiSeq v2 2x150 cartridge (per protocol)

• AFDIL whole genome procedure• Long PCR primers from Fendt et al., BMC Genomics 2009, 10:139• TaKaRa LA Taq (GC Buffer & BSA)• Kapa HyperPlus Library Kit• Illumina V3 2x300 cartridge

Pilot Data – Illumina Procedure Amplification

• PCR could be more robust• 18 of 95 (≈ 18 %) of samples - low yield

• Reproducible• Only one of two amplicons affected

• Not a sample quality issue

Amplicon 1 – First try

Amplicon 1 – Second try (re-PCR)

NTC Faile

d

Faile

d

NTC

Poor

Poor

1 2 3 4 5 6 7 8 9 10 11 SS

1 2 3 4 5 6 7 8 9 10 11 SS

≈ 10 kb

≈ 10 kb

SS = Size standard

Pilot Data – Illumina Procedure Amplification

• PCR could be more robust• 18 of 95 (≈ 18 %) of samples - low yield

• Reproducible• Amplicon 1 primer binding site mutation

• 16 of 18 low/neg samples had this • All haplogroup T (G1,888A)• HG-T frequency ≈ 10 % in Europeans

Amplicon 1 – First try

Amplicon 1 – Second try (re-PCR)

NTC Faile

d

Faile

d

NTC

Poor

Poor

1 2 3 4 5 6 7 8 9 10 11 SS

1 2 3 4 5 6 7 8 9 10 11 SS

SS = Size standard

≈ 10 kb

≈ 10 kb

AACTTTGCAAGGAGAGCCAA Primer binding site

Library QC – Illumina Procedure

• Nextera XT library• Default parameters per protocol

• 1 ng DNA• 5 minute fragmentation

≈ 760 bp

Sequencing Results - Illumina

• Most samples had > 99 % of mgGenome covered• Due to sensitivity of Nextera XT library prep• & Normalization of PCR input (amplicons 1 & 2 separately)

• Some gaps in coverage • Where amplification was poor

Gap areaShaded grey

Gap area

Sequencing Results - Illumina

• Some gaps in coverage • Frequent gaps in HV2 C-stretch• Even with good overall coverage

Pilot Data – AFDIL Procedure Amplification

• Primers from Fendt et al. 2009• TaKaRa LA Taq w/GC Buffer & BSA• 100 % of samples amplified

• Amplicon B gives higher yield than Amp A• Amp B contains control region

• Both amplicons ≈ 8 kb• Advantage of GC Buffer & BSA?

Amplicon A

Amplicon B

NTC

NTC

1 2 3 4 5 6 7 8 9 10 11 SS

1 2 3 4 5 6 7 8 9 10 11 SS

SS = Size standard

Protocol Optimization – Kapa HyperPlus

• What are the best parameters for library preparation?• Fragmentation time

• 5 min to 30 min• Input DNA

• 10 ng to 1000 ng (PCR product)

• Optimum library size • 2 x 300 bp cartridge planned• ≈ 450 bp library molecules

• 300 bp insert + 150 bp adaptors• No more than ≈ 1500 bp poor clustering

Kapa HyperPlus Technical Data Sheet (KR1145 v3.16)

≈ 450 bpTarget size

All reactions500 ng DNA input

10 min

20 min

30 min

Fragmentation TimeOptimization

≈ 450 bp

All reactions10 minfragmentation

10 ng

100 ng

500 ng

DNA InputOptimization

Optimized Conditions

• Fragmentation time = 15 minutes• DNA input ≈ 300 – 400 ng

Some residual adapter dimerTarget size450 bp

≈ 450 bp

All reactions10 min frag.,500 ng DNA

FullRx

HalfRx

Half ReactionTrial

Reaction kinetics not equal at half volume library construction.

Pilot Data – More Consistent Coverage DepthAFDIL method allows higher multiplexing with less likelihood of dropout sites

Illumina Whole mtGenome Method (Nextera Library Kit)

AFDIL Whole mtGenome Method (Kapa Hyper Plus Library Kit)

Pilot Data – Haplogroup Estimation

• No surprise haplogroupsSample Missing Mutations Private Mutations Haplogroup ContinentGT38086 none T16189C H1c21 Europe (H)GT38087 none none T2b6b EuropeGT38089 none T16189C J1c8a EuropeGT38091 none C10933T A15467G V EuropeGT38092 none C198T A9327G A13801G T15670C H5e1a1 Europe (H)GT38093 none none H1o EuropeGT38094 none A11252G H65 Europe (H)GT38095 -573.1C G709A C9727T I1a1b Europe (I1a1)GT38097 none G8027A G15301A K1a1b1 EuropeGT38098 A16183C -309.1C -309.2C C16111T T152C H1b1 EuropeGT38100 none -309.1C G4655A H1 EuropeGT38106 none T2416C A8817G H2a2a EuropeGT38107 none C3388A C8788T U5a1a1 EuropeGT38108 none T4373C T15313C H1+16189 EuropeJA44327 -573.1C G16474T I2 Europe (I)JM28315 -309.1C none K2a6 EuropeJT52345 none A16138G A73G H5a1c1a EuropeJT52346 none none H5g Europe

MT97121 none T16093C G7762A J1c2 EuropeMT97122 none none T2b2b EuropeMT97123 none A16158G T1a1 Europe (T1a)MT97124 T16093C -309.1C -524.3A -524.4C K1a EuropeMT97125 none T152C U5a2d1a Europe (U5a)

Cost analysis

Scenario 1: 32 samples per sequencing runThe S5XL is actually cheaper to use with smaller number of samples (chips are less expensive).

Note: the Ion Torrent product has a maximum of 32 barcodes if using Ion Chef DL8 library prepCost inflection point at number of samples = 47 - 48 where MiSeq becomes more cost effective, with certain assumptions.

Samples/runTotal samplesRuns

3266521S5MiSeq

243939.925899.1275

S5XLCost / unitCost / project486865.526790.655

Precision ID mtDNA Whole Genome Panel (P/N A30938 $3500.00 ea)$ 36.46$ 24,244.797210805.449089.7825

DL8 Library Kit (P/N A29024 $3900.80 ea)$ 121.90$ 81,063.509613731.049981.31

540 Chef Kit (P/N A30011 $6,132.80 ea)$ 766.60$ 8,049.30

Ion 540 Chip Kit (P/N A27766 $5,048.10 ea)$ 631.02$ 13,251.42

Total$ 102,364.22

MiSeqCost / unitCost / project

Clontech LA Taq Kit (P/N RR002M, 250 units, $287.00)$ 2.87$ 3,817.10

Fragment Analyzer kits for PCR quantitation (need ~ 3 runs/sample)$ 1,200.00$ 3,600.00

Nextera XT DNA Library Preparation kit (96 samples P/N FC-131-1096 $2,787.60 ea)$ 29.04$ 19,309.94

Nextera XT Barcode Kit v2 Set A (96 indices, 384 samples, P/N FC-131-2001, $909.88 ea)$ 2.37$ 1,575.70

MiSeq Cartridge v3, 600 cycle (P/N MS-102-3003, $1407.60 ea)$ 1,407.60$ 29,559.60

Total$ 57,862.34

Two caveats:

Labor - The Ion Chef would do all the library building. This is a big advantage, but without an army of Ion Chefs it would take a long time.

We haven't tried the Precision ID whole genome procedure before. Not sure how it functions. There's a whole lot of primer pairs in there.

Scenario 2: 96 samples per sequencing run

Alternate library prep uses AB Library Builder method with Fragment library kit and two amplicon strategy

Samples/runTotal samplesRuns

4866514

MiSeqCost / unitCost / project

Clontech LA Taq Kit (P/N RR002M, 250 units, $287.00)$ 2.87$ 3,817.10

Fragment Analyzer kits for PCR quantitation (need ~ 3 runs/sample)$ 1,200.00$ 3,600.00

Nextera XT DNA Library Preparation kit (96 samples P/N FC-131-1096 $2,787.60 ea)$ 29.04$ 19,309.94

Nextera XT Barcode Kit v2 Set A (96 indices, 384 samples, P/N FC-131-2001, $909.88 ea)$ 2.37$ 1,575.70

MiSeq Cartridge v3, 600 cycle (P/N MS-102-3003, $1407.60 ea)$ 1,407.60$ 19,706.40

Total$ 48,009.14

Relative Cost To Sequence on Two Platforms

S5244872963939.92000000000056865.5210805.44000000000213731.04MiSeq244872965899.12750000000056790.65499999999889089.78249999999939981.31

Cost 2

Scenario 1: 32 samples per sequencing run

Note: the Ion Torrent product has a maximum of 32 barcodes if using Ion Chef DL8 library prep

Prices per kit updated 8-23-18

S5XL - mtGenome, Automated Library PrepCost per kit# of samples per kitCost / 96 samplesCost / 32 samples

Precision ID mtDNA Whole Genome Panel (P/N A30938)358532$ 10,755.00$ 3,585.00

DL8 Library Kit (P/N A29024)374032$ 11,220.00$ 3,740.00

Precision ID Chef & Sequencing Kit (2 runs per initialization) P/N A332085340256$ 2,002.50$ 667.50

Ion 530 Chip Kit, 4 reactions (P/N A27763)2210128$ 1,657.50$ 552.50

Total$ 25,635.00$ 8,545.00

S5XL - mtGenome, Manual Library PrepCost per kit# of samples per kitCost / 96 samplesCost / 32 samples

Precision ID mtDNA Whole Genome Panel (P/N A30938)358532$ 10,755.00$ 3,585.00

Precision ID Library Kit, 96 reactions (P/N A26435)822096$ 8,220.00$ 2,740.00



Total$ 22,635.00$ 7,545.00

S5XL - Control Region, Automated Library PrepCost per kit# of samples per kitCost / 96 samplesCost / 32 samples

Precision ID mtDNA Control Region Panel (P/N A31443)107432$ 3,222.00$ 1,074.00

DL8 Library Kit (P/N A29024)374032$ 11,220.00$ 3,740.00



Total$ 18,102.00$ 4,960.00

S5XL - Control Region, Manual Library PrepCost per kit# of samples per kitCost / 96 samplesCost / 32 samples

Precision ID mtDNA Control Region Panel (P/N A31443)107496$ 1,074.00$ 358.00

Precision ID Library Kit, 96 reactions (P/N A26435)822096$ 8,220.00$ 2,740.00



Total$ 12,954.00$ 3,960.00

MiSeq - ILMN methodCost per kit# of samples per kitCost / 96 samplesCost / 32 samples

Clontech LA Taq Kit, (P/N RR002A, 250 units)287192$ 143.50$ 47.83

Fragment Analyzer Kit - High Molecular Weight, Standard Sensitivity, for PCR quantitation (P/N DNF-492)1250250$ 480.00$ 160.00

Fragment Analyzer Kit - NGS Fragment Analysis, High Sensitivity, for library QC (P/N DNF-474)1250500$ 240.00$ 80.00

Nextera XT DNA Library Preparation kit (96 samples P/N FC-131-1096)327096$ 3,270.00$ 1,090.00

Nextera XT Barcode Kit v2 Set A (96 indices, 384 samples, P/N FC-131-2001)1020384$ 255.00$ 85.00

MiSeq Cartridge v2, 300 cycle (P/N MS-102-2002)108048$ 2,160.00$ 720.00

Total$ 5,925.00$ 1,895.00

MiSeq - AFDIL methodCost per kit# of samples per kitCost / 96 samplesCost / 32 samples

Clontech LA Taq Kit, GC Buffer (P/N RR02AG, 250 units)143192$ 71.50$ 23.83

Applied Biosystems dNTP Mix (25 mM) (P/N N8080260)68.5192$ 34.25$ 11.42

Fragment Analyzer Kit - High Molecular Weight, Standard Sensitivity, for PCR quantitation (P/N DNF-492)1250250$ 480.00$ 160.00

Fragment Analyzer Kit - NGS Fragment Analysis, High Sensitivity, for library QC (P/N DNF-474)1250500$ 240.00$ 80.00

Kapa Biosystems HyperPlus Library Kit (PCR Free), 96 reactions (P/N KK8515)297696$ 2,976.00$ 992.00

Kapa Biosystems Dual Indexed Adapter Kit, 15 uM, 20 uL each (P/N KK8722)2304384$ 576.00$ 192.00

MiSeq Cartridge v3, 600 cycle (P/N MS-102-3003)158096$ 1,580.00$ 526.67

Total$ 5,372.00$ 1,710.67

Cost graph

Cost Per 96 Samples (Approximate)

S5XL Automated Library Prep$ 25,635

S5XL Manual Library Prep$ 12,954

MiSeq ILMN Method$ 5,925

MiSeq AFDIL Method$ 5,372

Cost Per 96 Samples (Approximate)S5XL Automated Library PrepS5XL Manual Library PrepMiSeq ILMN MethodMiSeq AFDIL Method256351295459255372

Gantt Chart

TaskDec 2017Jan 2018Feb 2018Mar 2018Apr 2018May 2018Jun 2018Jul 2018Aug 2018Sept 2018Oct 2018Nov 2018Dec 2018

Procure reagents

PCR Cauc 1

Library prep

Sequence

PCR Cauc 2

Library prep

Sequence

PCR Comb 1/2

Library prep

Sequence

PCR Cauc "Other", reruns

Library prep

Sequence

Data Analysis

Cauc 1 Variants, haplogroups

Cauc 2 Variants, haplogroups

Comb 1/2 Variants, haplogroups

Cauc "Other" Variants, haplogroups

Write Up

Data QC

Submit to EMPOP

Manuscript writing

Revisions

Submit to Journal

Budget

Caucasian samples (n = 440)Reactions = 480

Reagent namePart #CostNumber of samples / kitKits neededTotal costAlready have?More neededRemaining cost

Takara LA Taq with GC Buffer (125 unit)RR02AG$ 143.009610$ 1,430.0064$ 572.00

GeneAmp dNTP Blend (2.5 mM ea), ThermoFisherN8080260$ 68.5019210$ 685.0064$ 274.00

AATI High MW Fragment Analysis KitDNF-492$ 2,500.005002$ 5,000.0011$ 2,500.00

Kapa Hyper Prep (without amplification)KK8505$ 2,400.00965$ 12,000.0014$ 9,600.00

KAPA Pure BeadsKK8002$ 720.002502$ 1,440.0011$ 720.00

KAPA Dual-Indexed Adapter KitKK8722$ 2,304.003002$ 4,608.0011$ 2,304.00

AATI High Sensitivity NGS Fragment Analysis KitDNF-474$ 2,500.005001$ 2,500.0001$ 2,500.00

MiSeq V3 Reagent Kit (600 cycle)MS-102-3003$ 1,580.00965$ 7,900.0023$ 4,740.00

Total cost$ 35,563.00Remaining cost$ 23,210.00

Platemaps

C1GT38095JM28315MT97126MT97155TT51677UT58305GT38072GT36864JT51178MT94827MT9484295

GT38086GT38097JT52345MT97131MT97156TT51679UT58310GT38073GT36866JT51211MT94829MT94843

GT38087GT38098JT52346MT97136MT97158TT51680ZT81382GT38075GT36875MT94803MT94831MT94846

GT38089GT38100MT97121MT97139MT97159TT51682GT38065GT38076GT36877MT94807MT94833MT94848

GT38091GT38106MT97122MT97141PT86478TT51683GT38066GT38078GT36878MT94815MT94834MT94850

GT38092GT38107MT97123MT97145TT51669TT51684GT38067GT38081GT36884MT94817MT94835MT94853

GT38093GT38108MT97124MT97150TT51675TT51685GT38069GT38083GT36885MT94818MT94838MT94855

GT38094JA44327MT97125MT97152TT51676UT58303GT38070GC03394GT36886MT94826MT94839MT94858

C2MT97185MT97199TT51702WT52470WT52486ZT81380MT97167UA16894UA16921UT58298UT5831895

MT97173MT97186MT97200TT51703WT52471WT52490ZT81381OT07753UA16895UA16924UT58299UT58319

MT97176MT97187OT07803UT58333WT52472WT52493GT38114OT07760UA16896UA16927UT58300UT58320

MT97177MT97188TT51689UT58334WT52474ZC08844GT38119OT07767UA16897UA16928UT58301UT58321

MT97178MT97189TT51693UT58335WT52477ZT81337MT97163OT07776UA16899UA16929UT58302UT58324

MT97179MT97192TT51694UT58336WT52480ZT81342MT97164OT07785UA16903UC10177UT58314WA29566

MT97180MT97195TT51696UT58337WT52482ZT81372MT97165PT86536UA16908UC10178UT58315WA29572

MT97184MT97196TT51698WT52457WT52485ZT81377MT97166UA16891UA16918UT58295UT58317WA29583

CMB1UT57318WT51362WA29594JT51471OT05897PT84223PT84232GT37778GT37900TT51422ZT8078631

UT57300WT51342WT51373WA29612JT51499OT05898PT84224PT84234GT37812GT37913TT51435ZT80815

UT57301WT51343WT51378ZT81387OT05888OT05899PT84225PT84236GT37828JT52076TT51483ZT80826

UT57302WT51345WT51381MT94859OT05890OT05901PT84226PT84239ZT80932OT07280TT51511ZT80863

UT57303WT51354WT51386MT94866OT05892PT84214PT84227PT84240GT37862PT85612TT51530ZT80865

UT57310WT51355BC11352MT94868OT05893PT84215PT84228PT84241GT37864PT85658ZT80731ZT80869

UT57312WT51358MT97172MT94869OT05894PT84216PT84230PT84242GT37869TT51399ZT80737ZT80870

UT57317WT51359WA29584MT94875OT05896PT84222PT84231PT84243GT37888TT51407ZT80782ZT80925

CMB2MT94892TT50701UT57287PT84244ZT79619PT84212ZT79617Y6Y15Y23Y3141

MT94877MT94893TT50705UT57288PT84245PT84201PT84213ZT79618Y7Y16Y24Y32

MT94880PT83505TT50708UT57292PT84247PT84202PT84248GT37853Y8Y17Y25Y33

MT94882PT83535TT50720UT57293PT84256PT84206PT84249Y1Y9Y18Y26Y34

MT94883PT83538TT50721UT57299TT50913PT84208PT84251Y2Y10Y19Y27Y35

MT94884TT50697UT57281UT57635TT50916PT84209PT84252Y3Y12Y20Y28Y36

MT94886TT50698UT57283OT06795TT50922PT84210PT84253Y4Y13Y21Y29Y37

MT94888TT50700UT57286PC16856TT50923PT84211PT84254Y5Y14Y22Y30Y38262Should be 263

123456789101112

ABlankAF08CAF16CAF24CAF32CAF40CAF48CAF56CAF64CAF72CAF80CAF88C

BAF01CAF09CAF17CAF25CAF33CAF41CAF49CAF57CAF65CAF73CAF81CAF89C

CAF02CAF10CAF18CAF26CAF34CAF42CAF50CAF58CAF66CAF74CAF82CAF90C

DAF03CAF11CAF19CAF27CAF35CAF43CAF51CAF59CAF67CAF75CAF83CAF91C

EAF04CAF12CAF20CAF28CAF36CAF44CAF52CAF60CAF68CAF76CAF84CAF92C

FAF05CAF13CAF21CAF29CAF37CAF45CAF53CAF61CAF69CAF77CAF85CAF93C

GAF06CAF14CAF22CAF30CAF38CAF46CAF54CAF62CAF70CAF78CAF86CAF94CCaucasian Fathers

HAF07CAF15CAF23CAF31CAF39CAF47CAF55CAF63CAF71CAF79CAF87CAF95C90

123456789101112

ABlankC08CC16CC24CC32CC40CC48CC56CC64CC72CC80CC88C

BC01CC09CC17CC25CC33CC41CC49CC57CC65CC73CC81CC89C

CC02CC10CC18CC26CC34CC42CC50CC58CC66CC74CC82CC90C

DC03CC11CC19CC27CC35CC43CC51CC59CC67CC75CC83CC91C

EC04CC12CC20CC28CC36CC44CC52CC60CC68CC76CC84CC92C

FC05CC13CC21CC29CC37CC45CC53CC61CC69CC77CC85CC93C

GC06CC14CC22CC30CC38CC46CC54CC62CC70CC78CC86CC94CCaucasian Sons

HC07CC15CC23CC31CC39CC47CC55CC63CC71CC79CC87CC95C80

123456789101112

A

BAF96BAF96AAF96CAF96HC96BC96AC96CC96H

CAF97BAF97AAF97CAF97HC97BC97AC97CC97H

DAF98BAF98AAF98CAF98HC98BC98AC98CC98H

EAF99BAF99AAF99CAF99HC99BC99AC99CC99HAdditional Caucasian

FAF100BAF100AAF100CAF100HC100BC100AC100CC100H8

GAF101AC101A

H

Af AmerAsianCaucHispAf AmerAsianCaucHisp

FathersSonsTotal Caucasian mitogenomes

262 + 178 = 440

Progress - Fendt

PlateWellPopulationSample NameQuant Amp A (ng/uL)Quant Amp B (ng/uL)Amount of Amp1Amount of Amp2Total (ng)Use 1/2Library Conc (nmol/L)

C1A01CaucNTCPCR 4-2-18No ampNTC102ERROR:#VALUE!ERROR:#VALUE!

C1A02CaucGT38095PCR 4-2-1867.49191.341021057.5598528.7799165.042018/6/11 Use 10 uL of Amp A, 2 uL of Amp B in total volume of 100 uL.

C1A03CaucJM28315PCR 4-2-1861.60287.211021190.4286595.2143161.528Average concentration is 10 ng/uL (~600 ng Amp A, 500 ng Amp B) for C1 plate.

C1A04CaucMT97126PCR 4-2-1873.07214.361021159.4288579.7144143.005Use 35 uL in Frag Rx.

C1A05CaucMT97155PCR 4-2-1884.61214.561021275.229637.6145193.669Substitute 2392 A for A08 (GT38072) and 2392 B for A09 (GT36864), used for frag opt.

C1A06CaucTT51677PCR 4-2-1894.20241.181021424.369712.1845145.559

C1A07CaucUT58305PCR 4-2-1841.12192.10102795.3452397.6726127.02

C1A08CaucGT38072PCR 4-2-18124.51255.661021756.4354878.217799.813WellSample IDPeak IDSize (bp)ng/ulUse PCRH2O

C1A09CaucGT36864PCR 4-2-18104.59273.591021593.0238796.5119153.926A1SampA16885389.47392392 AFendt A5.673.7

C1A10CaucJT51178PCR 4-2-1825.21167.41102586.8896293.444877.133A2SampA26876572.82382392 BFendt A6.981.0

C1A11CaucMT94827PCR 4-2-1828.28191.60102665.9738332.9869147.072A5SampA53933824.13842392 AFendt B20.7

C1A12CaucMT94842PCR 4-2-1819.67267.63102731.9532365.9766247.448A6SampA63894241.14232392 BFendt B12.2

C1B01CaucGT38086PCR 4-2-1869.70286.771021270.5776635.2888105.214

C1B02CaucGT38097PCR 4-2-1869.27276.671021246.0026623.0013191.778

C1B03CaucJT52345PCR 4-2-1855.06234.201021018.9648509.4824125.385

C1B04CaucMT97131PCR 4-2-1860.99217.811021045.5468522.7734150.042018/06/12 based on average of 170 nM library concentration:

C1B05CaucMT97156PCR 4-2-1849.06181.24102853.0652426.5326168.23Pool all 96 libraries

C1B06CaucTT51679PCR 4-2-1859.14243.631021078.7084539.3542153.954Dilute to 4 nM, follow ILMN denature and dilute guide.

C1B07CaucUT58310PCR 4-2-1821.36186.27102586.1442293.0721131.7Initial concFinal ConcFinal VolInitial library VolPlus Diluent

C1B08CaucGT38073PCR 4-2-1867.14232.111021135.576567.788209.35617042004.71195.29

C1B09CaucGT36866PCR 4-2-1882.75267.401021362.2578681.1289272.39

C1B10CaucJT51211PCR 4-2-1868.11203.571021088.2846544.1423153.786

C1B11CaucMT94829PCR 4-2-1830.57168.87102643.4624321.7312149.269

C1B12CaucMT94843PCR 4-2-1812.00169.02102458.0152229.0076133.957

C1C01CaucGT38087PCR 4-2-1866.20288.911021239.8766619.938380.684

C1C02CaucGT38098PCR 4-2-1857.82264.221021106.666553.333148.421

C1C03CaucJT52346PCR 4-2-1865.52258.231021171.6316585.8158125.232

C1C04CaucMT97136PCR 4-2-1861.94285.421021190.234595.117146.537

C1C05CaucMT97158PCR 4-2-1861.74281.871021181.1798590.5899159.405

C1C06CaucTT51680PCR 4-2-1859.07223.251021037.2294518.6147125.865

C1C07CaucZT81382PCR 4-2-1865.51265.111021185.369592.6845189.598

C1C08CaucGT38075PCR 4-2-1887.82283.011021444.2656722.1328213.813

C1C09CaucGT36875PCR 4-2-1892.39255.441021434.7416717.3708223.184

C1C10CaucMT94803PCR 4-2-1828.92217.52102724.287362.143590.004

C1C11CaucMT94831PCR 4-2-1855.23219.71102991.7334495.8667187.873

C1C12CaucMT94846PCR 4-2-1833.59276.29102888.4346444.2173253.346

C1D01CaucGT38089PCR 4-2-1866.34285.641021234.6498617.324994.631

C1D02CaucGT38100PCR 4-2-1875.13294.381021340.0998670.0499189.04

C1D03CaucMT97121PCR 4-2-1878.33195.471021174.1902587.0951157.048

C1D04CaucMT97139PCR 4-2-1848.30304.421021091.8476545.9238147.929

C1D05CaucMT97159PCR 4-2-1844.96188.87102827.369413.6845153.287

C1D06CaucTT51682PCR 4-2-1899.57298.861021593.4514796.7257250.823

C1D07CaucGT38065PCR 4-2-1884.80219.921021287.8198643.9099239.535

C1D08CaucGT38076PCR 4-2-1871.91253.211021225.5036612.7518238.511

C1D09CaucGT36877PCR 4-2-1895.62280.561021517.3314758.6657289.015

C1D10CaucMT94807PCR 4-2-18109.89284.301021667.5136833.7568242.782

C1D11CaucMT94833PCR 4-2-1819.61170.65102537.3644268.6822

C1D12CaucMT94848PCR 4-2-1825.90285.48102829.933414.9665212.181

C1E01CaucGT38091PCR 4-2-1884.51356.811021558.7192779.359686.897

C1E02CaucGT38106PCR 4-2-1867.65291.761021260.0044630.0022170.874

C1E03CaucMT97122PCR 4-2-1855.14336.631021224.6842612.3421117.7

C1E04CaucMT97141PCR 4-2-1862.49327.461021279.8442639.9221153.259

C1E05CaucPT86478PCR 4-2-1850.39223.32102950.5654475.2827138.508

C1E06CaucTT51683PCR 4-2-1864.90241.461021131.8958565.9479151.047

C1E07CaucGT38066PCR 4-2-1892.53326.561021578.4664789.2332239.912

C1E08CaucGT38078PCR 4-2-1882.05290.711021401.9124700.9562200.925

C1E09CaucGT36878PCR 4-2-1896.34233.351021430.0748715.0374200.483

C1E10CaucMT94815PCR 4-2-1889.09318.711021528.3052764.1526190.944

C1E11CaucMT94834PCR 4-2-1863.60288.521021213.0878606.5439221.239

C1E12CaucMT94850PCR 4-2-1822.81284.85102797.752398.876230.406

C1F01CaucGT38092PCR 4-2-1849.36268.621021030.8226515.411363.938

C1F02CaucGT38107PCR 4-2-1870.28237.121021177.0086588.5043175.192

C1F03CaucMT97123PCR 4-2-1858.57232.061021049.829524.9145117.907

C1F04CaucMT97145PCR 4-2-1861.16294.251021200.1258600.0629146.126

C1F05CaucTT51669PCR 4-2-1841.67254.03102924.7366462.3683126.545

C1F06CaucTT51684PCR 4-2-1855.65226.461021009.4272504.7136146.724

C1F07CaucGT38067PCR 4-2-1879.13238.311021267.8842633.9421213.167

C1F08CaucGT38081PCR 4-2-1870.72242.121021191.404595.702205.687

C1F09CaucGT36884PCR 4-2-1876.29304.621021372.1154686.0577220.416

C1F10CaucMT94817PCR 4-2-1888.93283.771021456.8618728.4309204.126

C1F11CaucMT94835PCR 4-2-1850.75191.34102890.2068445.1034192.665

C1F12CaucMT94853PCR 4-2-180.57283.92102573.5094286.7547223.42

C1G01CaucGT38093PCR 4-2-1895.35280.891021515.2748757.6374106.875

C1G02CaucGT38108PCR 4-2-1832.21228.14102778.3722389.1861107.631

C1G03CaucMT97124PCR 4-2-1877.07235.401021241.4802620.7401156.672

C1G04CaucMT97150PCR 4-2-1859.66242.461021081.569540.7845139.678

C1G05CaucTT51675PCR 4-2-1843.06238.10102906.772453.386

C1G06CaucTT51685PCR 4-2-1859.66227.821021052.2914526.1457163.171

C1G07CaucGT38069PCR 4-2-18103.26353.021021738.6692869.3346288.833

C1G08CaucGT38083PCR 4-2-1858.60217.071021020.1914510.0957169.224

C1G09CaucGT36885PCR 4-2-1890.16255.461021412.4738706.2369279.958

C1G10CaucMT94818PCR 4-2-1895.22299.931021552.0812776.0406244.366

C1G11CaucMT94838PCR 4-2-180.245.2110212.78846.3942Size of B amplicon not consistent2.056

C1G12CaucMT94855PCR 4-2-1835.59293.19102942.282471.141291.885

C1H01CaucGT38094PCR 4-2-1826.80231.20102730.4192365.209671.427

C1H02CaucJA44327PCR 4-2-1832.27214.91102752.5162376.2581178.969

C1H03CaucMT97125PCR 4-2-1831.44247.42102809.2154404.6077157.39

C1H04CaucMT97152PCR 4-2-1829.58217.10102730.0258365.0129149.256

C1H05CaucTT51676PCR 4-2-1835.30155.40102663.8068331.9034132.289

C1H06CaucUT58303PCR 4-2-1836.43188.56102741.4458370.7229129.69

C1H07CaucGT38070PCR 4-2-1844.88265.85102980.5456490.2728261.257

C1H08CaucGC03394PCR 4-2-1836.30234.86102832.6916416.3458217.587

C1H09CaucGT36886PCR 4-2-1832.38185.79102695.335347.6675192.389

C1H10CaucMT94826PCR 4-2-1816.64231.74102629.831314.9155170.251

C1H11CaucMT94839PCR 4-2-180.34241.09102485.5516242.7758188.405

C1H12CaucMT94858PCR 4-2-1862.85281.111021190.7072595.3536155.469

Average58.90247.300.2381711494Average1083.60170.5Average

Min0.245.21291.9Max

Max124.51356.812.1Min

Quant Amp A (ng/uL)Quant Amp B (ng/uL)

NTC2018-08-20 Combine AmpA/AmpB in 1:3 ratio (average is 27ng & 9 ng/ul)

C2A02CaucMT97185PCR 8-10-1817.363.83Mix 5 ul Amp A + 15 ul Amp B --> ((5*27)+(15*9)/20) = 13.5 ng/ul

C2A03CaucMT97199PCR 8-10-1827.5211.46Use 17.5 uL in Frag Rx. (Note this will be below desired 350 ng input (@ ~ 235 ng).)

C2A04CaucTT51702PCR 8-10-1814.973.20Run SRM 2391d components A-E (PCR 8/8/2018)

C2A05CaucWT52470PCR 8-10-1829.3913.15

C2A06CaucWT52486PCR 8-10-1824.1012.82

C2A07CaucZT81380PCR 8-10-1830.489.32WellSample IDPeak IDSize (bp)ng/ulUse PCRH2O

C2A08CaucMT97167PCR 8-10-1818.554.45

C2A09CaucUA16894PCR 8-10-1833.006.89

C2A10CaucUA16921PCR 8-10-1833.638.97

C2A11CaucUT58298PCR 8-10-1846.439.96

C2A12CaucUT58318PCR 8-10-1826.544.52

C2B01CaucMT97173PCR 8-10-1826.709.74

C2B02CaucMT97186PCR 8-10-1829.829.61

C2B03CaucMT97200PCR 8-10-1821.278.96

C2B04CaucTT51703PCR 8-10-1820.208.39

C2B05CaucWT52471PCR 8-10-1825.9915.67

C2B06CaucWT52490PCR 8-10-1819.8610.19

C2B07CaucZT81381PCR 8-10-189.661.31

C2B08CaucOT07753PCR 8-10-1826.9810.16

C2B09CaucUA16895PCR 8-10-1831.075.362018/06/12 based on average of 170 nM library concentration:

C2B10CaucUA16924PCR 8-10-1821.1510.49Pool all 96 libraries

C2B11CaucUT58299PCR 8-10-1841.289.90Dilute to 4 nM, follow ILMN denature and dilute guide.

C2B12CaucUT58319PCR 8-10-1835.2013.20Initial concFinal ConcFinal VolInitial library VolPlus Diluent

C2C01CaucMT97176PCR 8-10-1826.246.7817042004.71195.29

C2C02CaucMT97187PCR 8-10-1827.3811.74

C2C03CaucOT07803PCR 8-10-1822.403.42

C2C04CaucUT58333PCR 8-10-1815.465.28

C2C05CaucWT52472PCR 8-10-1818.514.86

C2C06CaucWT52493PCR 8-10-1820.176.59

C2C07CaucGT38114PCR 8-10-1821.2111.46

C2C08CaucOT07760PCR 8-10-1834.6015.05

C2C09CaucUA16896PCR 8-10-1825.526.74

C2C10CaucUA16927PCR 8-10-1823.447.92

C2C11CaucUT58300PCR 8-10-1834.2212.75

C2C12CaucUT58320PCR 8-10-1825.517.52

C2D01CaucMT97177PCR 8-10-1826.057.17

C2D02CaucMT97188PCR 8-10-1834.327.59

C2D03CaucTT51689PCR 8-10-1826.9610.85

C2D04CaucUT58334PCR 8-10-1822.377.76

C2D05CaucWT52474PCR 8-10-1819.116.92

C2D06CaucZC08844PCR 8-10-1846.0615.87

C2D07CaucGT38119PCR 8-10-1842.7919.08

C2D08CaucOT07767PCR 8-10-1827.564.68

C2D09CaucUA16897PCR 8-10-1823.237.63

C2D10CaucUA16928PCR 8-10-1823.817.12

C2D11CaucUT58301PCR 8-10-1845.9612.28

C2D12CaucUT58321PCR 8-10-1835.3110.08

C2E01CaucMT97178PCR 8-10-1831.478.95

C2E02CaucMT97189PCR 8-10-1827.2613.11

C2E03CaucTT51693PCR 8-10-1817.765.87

C2E04CaucUT58335PCR 8-10-1821.424.01

C2E05CaucWT52477PCR 8-10-1821.566.86

C2E06CaucZT81337PCR 8-10-1834.4411.99

C2E07CaucMT97163PCR 8-10-1836.5111.84

C2E08CaucOT07776PCR 8-10-1821.446.61

C2E09CaucUA16899PCR 8-10-1823.894.85

C2E10CaucUA16929PCR 8-10-1830.135.52

C2E11CaucUT58302PCR 8-10-1833.3514.29

C2E12CaucUT58324PCR 8-10-1832.799.29

C2F01CaucMT97179PCR 8-10-1825.369.76

C2F02CaucMT97192PCR 8-10-1819.224.64

C2F03CaucTT51694PCR 8-10-1822.308.04

C2F04CaucUT58336PCR 8-10-1818.965.01

C2F05CaucWT52480PCR 8-10-1829.1212.16

C2F06CaucZT81342PCR 8-10-1833.839.98

C2F07CaucMT97164PCR 8-10-1833.1115.22

C2F08CaucOT07785PCR 8-10-1823.578.18

C2F09CaucUA16903PCR 8-10-1814.944.52

C2F10CaucUC10177PCR 8-10-1828.8011.65

C2F11CaucUT58314PCR 8-10-1827.528.48

C2F12CaucWA29566PCR 8-10-1846.4615.16

C2G01CaucMT97180PCR 8-10-1819.368.16

C2G02CaucMT97195PCR 8-10-1825.403.60

C2G03CaucTT51696PCR 8-10-1828.358.85

C2G04CaucUT58337PCR 8-10-1818.007.60

C2G05CaucWT52482PCR 8-10-1815.606.08

C2G06CaucZT81372PCR 8-10-1821.673.53

C2G07CaucMT97165PCR 8-10-1822.316.79

C2G08CaucPT86536PCR 8-10-1822.634.42

C2G09CaucUA16908PCR 8-10-1815.036.24

C2G10CaucUC10178PCR 8-10-1824.148.96

C2G11CaucUT58315PCR 8-10-1833.7311.47

C2G12CaucWA29572PCR 8-10-1823.429.49

C2H01CaucMT97184PCR 8-10-1821.365.05

C2H02CaucMT97196PCR 8-10-1825.689.58

C2H03CaucTT51698PCR 8-10-1823.477.43

C2H04CaucWT52457PCR 8-10-1839.979.28

C2H05CaucWT52485PCR 8-10-1822.6213.65

C2H06CaucZT81377PCR 8-10-1825.134.77

C2H07CaucMT97166PCR 8-10-1839.519.13

C2H08CaucUA16891PCR 8-10-1819.464.20

C2H09CaucUA16918PCR 8-10-1832.478.76

C2H10CaucUT58295PCR 8-10-1838.8418.29

C2H11CaucUT58317PCR 8-10-1826.535.90

C2H12CaucWA29583PCR 8-10-1819.707.78

Average26.738.67

Min9.661.31

Max46.4619.08

Combo1A02CaucUT57318

Combo1A03CaucWT51362

Combo1A04CaucWA29594

Combo1A05AAJT51471

Combo1A06AAOT05897

Combo1A07AAPT84223

Combo1A08AAPT84232

Combo1A09HispGT37778


Combo1A11HispTT51422

Combo1A12HispZT80786

Combo1B01CaucUT57300

Combo1B02CaucWT51342


Combo1B04CaucWA29612

Combo1B05AAJT51499

Combo1B06AAOT05898

Combo1B07AAPT84224

Combo1B08AAPT84234

Combo1B09HispGT37812


Combo1B11HispTT51435

Combo1B12HispZT80815

Combo1C01CaucUT57301

Combo1C02CaucWT51343


Combo1C04CaucZT81387

Combo1C05AAOT05888

Combo1C06AAOT05899

Combo1C07AAPT84225

Combo1C08AAPT84236

Combo1C09HispGT37828

Combo1C10HispJT52076

Combo1C11HispTT51483

Combo1C12HispZT80826

Combo1D01CaucUT57302

Combo1D02CaucWT51345


Combo1D04CaucMT94859

Combo1D05AAOT05890

Combo1D06AAOT05901

Combo1D07AAPT84226

Combo1D08AAPT84239

Combo1D09HispZT80932

Combo1D10HispOT07280

Combo1D11HispTT51511


Combo1E01CaucUT57303

Combo1E02CaucWT51354


Combo1E04CaucMT94866

Combo1E05AAOT05892

Combo1E06AAPT84214

Combo1E07AAPT84227

Combo1E08AAPT84240

Combo1E09HispGT37862

Combo1E10HispPT85612

Combo1E11HispTT51530

Combo1E12HispZT80865

Combo1F01CaucUT57310

Combo1F02CaucWT51355

Combo1F03CaucBC11352

Combo1F04CaucMT94868

Combo1F05AAOT05893

Combo1F06AAPT84215

Combo1F07AAPT84228

Combo1F08AAPT84241

Combo1F09HispGT37864

Combo1F10HispPT85658

Combo1F11HispZT80731


Combo1G01CaucUT57312

Combo1G02CaucWT51358

Combo1G03CaucMT97172


Combo1G05AAOT05894

Combo1G06AAPT84216

Combo1G07AAPT84230

Combo1G08AAPT84242

Combo1G09HispGT37869

Combo1G10HispTT51399

Combo1G11HispZT80737


Combo1H01CaucUT57317

Combo1H02CaucWT51359

Combo1H03CaucWA29584

Combo1H04CaucMT94875

Combo1H05AAOT05896

Combo1H06AAPT84222

Combo1H07AAPT84231

Combo1H08AAPT84243

Combo1H09HispGT37888

Combo1H10HispTT51407

Combo1H11HispZT80782


Combo2A02CaucMT94892

Combo2A03CaucTT50701


Combo2A05AAPT84244

Combo2A06AAZT79619

Combo2A07AAPT84212

Combo2A08AAZT79617

Combo2A09CaucY6

Combo2A10AAY15

Combo2A11HispY23

Combo2A12CaucY31

Combo2B01CaucMT94877


Combo2B03CaucTT50705


Combo2B05AAPT84245

Combo2B06AAPT84201

Combo2B07AAPT84213

Combo2B08AAZT79618

Combo2B09CaucY7

Combo2B10AAY16

Combo2B11HispY24

Combo2B12CaucY32

Combo2C01CaucMT94880

Combo2C02CaucPT83505

Combo2C03CaucTT50708


Combo2C05AAPT84247

Combo2C06AAPT84202

Combo2C07AAPT84248


Combo2C09CaucY8

Combo2C10AAY17

Combo2C11HispY25

Combo2C12AAY33


Combo2D02CaucPT83535

Combo2D03CaucTT50720


Combo2D05AAPT84256

Combo2D06AAPT84206

Combo2D07AAPT84249

Combo2D08CaucY1

Combo2D09CaucY9

Combo2D10AAY18

Combo2D11HispY26

Combo2D12AAY34


Combo2E02CaucPT83538

Combo2E03CaucTT50721


Combo2E05AATT50913

Combo2E06AAPT84208

Combo2E07AAPT84251

Combo2E08CaucY2

Combo2E09CaucY10

Combo2E10AAY19

Combo2E11HispY27

Combo2E12AAY35


Combo2F02CaucTT50697


Combo2F04AsianUT57635

Combo2F05AATT50916

Combo2F06AAPT84209

Combo2F07AAPT84252

Combo2F08CaucY3

Combo2F09CaucY12

Combo2F10HispY20

Combo2F11HispY28

Combo2F12AAY36


Combo2G02CaucTT50698


Combo2G04AsianOT06795

Combo2G05AATT50922

Combo2G06AAPT84210

Combo2G07AAPT84253

Combo2G08CaucY4

Combo2G09AAY13

Combo2G10HispY21

Combo2G11HispY29

Combo2G12AAY37


Combo2H02CaucTT50700


Combo2H04AsianPC16856

Combo2H05AATT50923

Combo2H06AAPT84211

Combo2H07AAPT84254

Combo2H08CaucY5

Combo2H09AAY14

Combo2H10HispY22

Combo2H11HispY30

Combo2H12HispY38

BlankPCR 2018-08-08

AF01CPCR 2018-08-08Failed to amplify










































AF43C

AF44C

AF45C

AF46C

AF47C

AF48C

AF49C

AF50C

AF51C

AF52C

AF53C

AF54C

AF55C

AF56C

AF57C

AF58C

AF59C

AF60C

AF61C

AF62C

AF63C

AF64C

AF65C

AF66C

AF67C

AF68C

AF69C

AF70C

AF71C

AF72C

AF73C

AF74C

AF75C

AF76C

AF77C

AF78C

AF79C

AF80C

AF81C

AF82C

AF83C

AF84C

AF85C

AF86C

AF87C

AF88C

AF89C

AF90C

AF91C

AF92C

AF93C

AF94C

AF95C

Samplesheets

A1Empty_A1

C1GT38095JM28315MT97126MT97155TT51677UT58305GT38072GT36864JT51178MT94827MT9484295C1A02CaucGT38095A2Empty_A2

GT38086GT38097JT52345MT97131MT97156TT51679UT58310GT38073GT36866JT51211MT94829MT94843C1A03CaucJM28315A3Empty_A3

GT38087GT38098JT52346MT97136MT97158TT51680ZT81382GT38075GT36875MT94803MT94831MT94846C1A04CaucMT97126A4Empty_A4

GT38089GT38100MT97121MT97139MT97159TT51682GT38065GT38076GT36877MT94807MT94833MT94848C1A05CaucMT97155A5Empty_A5

GT38091GT38106MT97122MT97141PT86478TT51683GT38066GT38078GT36878MT94815MT94834MT94850C1A06CaucTT51677A6Empty_A6

GT38092GT38107MT97123MT97145TT51669TT51684GT38067GT38081GT36884MT94817MT94835MT94853C1A07CaucUT58305A7Empty_A7

GT38093GT38108MT97124MT97150TT51675TT51685GT38069GT38083GT36885MT94818MT94838MT94855C1A08CaucGT38072A8Empty_A8

GT38094JA44327MT97125MT97152TT51676UT58303GT38070GC03394GT36886MT94826MT94839MT94858C1A09CaucGT36864A9Empty_A9

C1A10CaucJT51178A10Empty_A10

C2MT97185MT97199TT51702WT52470WT52486ZT81380MT97167UA16894UA16921UT58298UT5831895C1A11CaucMT94827A11Empty_A11

MT97173MT97186MT97200TT51703WT52471WT52490ZT81381OT07753UA16895UA16924UT58299UT58319C1A12CaucMT94842A12Empty_A12

MT97176MT97187OT07803UT58333WT52472WT52493GT38114OT07760UA16896UA16927UT58300UT58320C1B01CaucGT38086B1Empty_B1

MT97177MT97188TT51689UT58334WT52474ZC08844GT38119OT07767UA16897UA16928UT58301UT58321C1B02CaucGT38097B2Empty_B2

MT97178MT97189TT51693UT58335WT52477ZT81337MT97163OT07776UA16899UA16929UT58302UT58324C1B03CaucJT52345B3Empty_B3

MT97179MT97192TT51694UT58336WT52480ZT81342MT97164OT07785UA16903UC10177UT58314WA29566C1B04CaucMT97131B4Empty_B4

MT97180MT97195TT51696UT58337WT52482ZT81372MT97165PT86536UA16908UC10178UT58315WA29572C1B05CaucMT97156B5Empty_B5

MT97184MT97196TT51698WT52457WT52485ZT81377MT97166UA16891UA16918UT58295UT58317WA29583C1B06CaucTT51679B6Empty_B6

C1B07CaucUT58310B7Empty_B7

CMB1UT57318WT51362WA29594JT51471OT05897PT84223PT84232GT37778GT37900TT51422ZT8078631C1B08CaucGT38073B8Empty_B8

UT57300WT51342WT51373WA29612JT51499OT05898PT84224PT84234GT37812GT37913TT51435ZT80815C1B09CaucGT36866B9Empty_B9

UT57301WT51343WT51378ZT81387OT05888OT05899PT84225PT84236GT37828JT52076TT51483ZT80826C1B10CaucJT51211B10Empty_B10

UT57302WT51345WT51381MT94859OT05890OT05901PT84226PT84239ZT80932OT07280TT51511ZT80863C1B11CaucMT94829B11Empty_B11

UT57303WT51354WT51386MT94866OT05892PT84214PT84227PT84240GT37862PT85612TT51530ZT80865C1B12CaucMT94843B12Empty_B12

UT57310WT51355BC11352MT94868OT05893PT84215PT84228PT84241GT37864PT85658ZT80731ZT80869C1C01CaucGT38087C1Empty_C1

UT57312WT51358MT97172MT94869OT05894PT84216PT84230PT84242GT37869TT51399ZT80737ZT80870C1C02CaucGT38098C2Empty_C2

UT57317WT51359WA29584MT94875OT05896PT84222PT84231PT84243GT37888TT51407ZT80782ZT80925C1C03CaucJT52346C3Empty_C3

C1C04CaucMT97136C4Empty_C4

CMB2MT94892TT50701UT57287PT84244ZT79619PT84212ZT79617Y6Y15Y23Y3144C1C05CaucMT97158C5Empty_C5

MT94877MT94893TT50705UT57288PT84245PT84201PT84213ZT79618Y7Y16Y24Y32C1C06CaucTT51680C6Empty_C6

MT94880PT83505TT50708UT57292PT84247PT84202PT84248GT37853Y8Y17Y25Y33C1C07CaucZT81382C7Empty_C7

MT94882PT83535TT50720UT57293PT84256PT84206PT84249Y1Y9Y18Y26Y34C1C08CaucGT38075C8Empty_C8

MT94883PT83538TT50721UT57299TT50913PT84208PT84251Y2Y10Y19Y27Y35C1C09CaucGT36875C9Empty_C9

MT94884TT50697UT57281UT57635TT50916PT84209PT84252Y3Y12Y20Y28Y36C1C10CaucMT94803C10Empty_C10

MT94886TT50698UT57283OT06795TT50922PT84210PT84253Y4Y13Y21Y29Y37C1C11CaucMT94831C11Empty_C11

MT94888TT50700UT57286PC16856TT50923PT84211PT84254Y5Y14Y22Y30Y38265Should be 263C1C12CaucMT94846C12Empty_C12

C1D01CaucGT38089D1Empty_D1


C1D03CaucMT97121D3Empty_D3



C1D06CaucTT51682D6Empty_D6







C1E01CaucGT38091E1Empty_E1


C1E03CaucMT97122E3Empty_E3


C1E05CaucPT86478E5Empty_E5

C1E06CaucTT51683E6Empty_E6







C1F01CaucGT38092F1Empty_F1


C1F03CaucMT97123F3Empty_F3


C1F05CaucTT51669F5Empty_F5

C1F06CaucTT51684F6Empty_F6







C1G01CaucGT38093G1Empty_G1


C1G03CaucMT97124G3Empty_G3


C1G05CaucTT51675G5Empty_G5

C1G06CaucTT51685G6Empty_G6







C1H01CaucGT38094H1Empty_H1

C1H02CaucJA44327H2Empty_H2

C1H03CaucMT97125H3Empty_H3


C1H05CaucTT51676H5Empty_H5

C1H06CaucUT58303H6Empty_H6


C1H08CaucGC03394H8Empty_H8





C2A02CaucMT97185

C2A03CaucMT97199

C2A04CaucTT51702

C2A05CaucWT52470

C2A06CaucWT52486

C2A07CaucZT81380

C2A08CaucMT97167

C2A09CaucUA16894

C2A10CaucUA16921

C2A11CaucUT58298

C2A12CaucUT58318

C2B01CaucMT97173

C2B02CaucMT97186

C2B03CaucMT97200

C2B04CaucTT51703

C2B05CaucWT52471

C2B06CaucWT52490

C2B07CaucZT81381

C2B08CaucOT07753

C2B09CaucUA16895

C2B10CaucUA16924

C2B11CaucUT58299

C2B12CaucUT58319

C2C01CaucMT97176

C2C02CaucMT97187

C2C03CaucOT07803

C2C04CaucUT58333

C2C05CaucWT52472

C2C06CaucWT52493

C2C07CaucGT38114

C2C08CaucOT07760

C2C09CaucUA16896

C2C10CaucUA16927

C2C11CaucUT58300

C2C12CaucUT58320

C2D01CaucMT97177

C2D02CaucMT97188

C2D03CaucTT51689

C2D04CaucUT58334

C2D05CaucWT52474

C2D06CaucZC08844

C2D07CaucGT38119

C2D08CaucOT07767

C2D09CaucUA16897

C2D10CaucUA16928

C2D11CaucUT58301

C2D12CaucUT58321

C2E01CaucMT97178

C2E02CaucMT97189

C2E03CaucTT51693

C2E04CaucUT58335

C2E05CaucWT52477

C2E06CaucZT81337

C2E07CaucMT97163

C2E08CaucOT07776

C2E09CaucUA16899

C2E10CaucUA16929

C2E11CaucUT58302

C2E12CaucUT58324

C2F01CaucMT97179

C2F02CaucMT97192

C2F03CaucTT51694

C2F04CaucUT58336

C2F05CaucWT52480

C2F06CaucZT81342

C2F07CaucMT97164

C2F08CaucOT07785

C2F09CaucUA16903

C2F10CaucUC10177

C2F11CaucUT58314

C2F12CaucWA29566

C2G01CaucMT97180

C2G02CaucMT97195

C2G03CaucTT51696

C2G04CaucUT58337

C2G05CaucWT52482

C2G06CaucZT81372

C2G07CaucMT97165

C2G08CaucPT86536

C2G09CaucUA16908

C2G10CaucUC10178

C2G11CaucUT58315

C2G12CaucWA29572

C2H01CaucMT97184

C2H02CaucMT97196

C2H03CaucTT51698

C2H04CaucWT52457

C2H05CaucWT52485

C2H06CaucZT81377

C2H07CaucMT97166

C2H08CaucUA16891

C2H09CaucUA16918

C2H10CaucUT58295

C2H11CaucUT58317

C2H12CaucWA29583


Combo1A03CaucWT51362

Combo1A04CaucWA29594

Combo1A05AAJT51471

Combo1A06AAOT05897

Combo1A07AAPT84223

Combo1A08AAPT84232



Combo1A11HispTT51422

Combo1A12HispZT80786




Combo1B04CaucWA29612

Combo1B05AAJT51499

Combo1B06AAOT05898

Combo1B07AAPT84224

Combo1B08AAPT84234



Combo1B11HispTT51435

Combo1B12HispZT80815




Combo1C04CaucZT81387

Combo1C05AAOT05888

Combo1C06AAOT05899

Combo1C07AAPT84225

Combo1C08AAPT84236


Combo1C10HispJT52076

Combo1C11HispTT51483

Combo1C12HispZT80826





Combo1D05AAOT05890

Combo1D06AAOT05901

Combo1D07AAPT84226

Combo1D08AAPT84239


Combo1D10HispOT07280

Combo1D11HispTT51511






Combo1E05AAOT05892

Combo1E06AAPT84214

Combo1E07AAPT84227

Combo1E08AAPT84240

Combo1E09HispGT37862

Combo1E10HispPT85612

Combo1E11HispTT51530

Combo1E12HispZT80865


Combo1F02CaucWT51355

Combo1F03CaucBC11352


Combo1F05AAOT05893

Combo1F06AAPT84215

Combo1F07AAPT84228

Combo1F08AAPT84241

Combo1F09HispGT37864

Combo1F10HispPT85658




Combo1G02CaucWT51358



Combo1G05AAOT05894

Combo1G06AAPT84216

Combo1G07AAPT84230

Combo1G08AAPT84242

Combo1G09HispGT37869

Combo1G10HispTT51399




Combo1H02CaucWT51359

Combo1H03CaucWA29584


Combo1H05AAOT05896

Combo1H06AAPT84222

Combo1H07AAPT84231

Combo1H08AAPT84243

Combo1H09HispGT37888

Combo1H10HispTT51407



Combo2A02CaucMT94892

Combo2A03CaucTT50701


Combo2A05AAPT84244

Combo2A06AAZT79619

Combo2A07AAPT84212

Combo2A08AAZT79617

Combo2A09CaucY6

Combo2A10AAY15

Combo2A11HispY23

Combo2A12CaucY31



Combo2B03CaucTT50705


Combo2B05AAPT84245

Combo2B06AAPT84201

Combo2B07AAPT84213

Combo2B08AAZT79618

Combo2B09CaucY7

Combo2B10AAY16

Combo2B11HispY24

Combo2B12CaucY32

Combo2C01CaucMT94880

Combo2C02CaucPT83505

Combo2C03CaucTT50708


Combo2C05AAPT84247

Combo2C06AAPT84202

Combo2C07AAPT84248


Combo2C09CaucY8

Combo2C10AAY17

Combo2C11HispY25

Combo2C12AAY33


Combo2D02CaucPT83535

Combo2D03CaucTT50720


Combo2D05AAPT84256

Combo2D06AAPT84206

Combo2D07AAPT84249

Combo2D08CaucY1

Combo2D09CaucY9

Combo2D10AAY18

Combo2D11HispY26

Combo2D12AAY34


Combo2E02CaucPT83538

Combo2E03CaucTT50721


Combo2E05AATT50913

Combo2E06AAPT84208

Combo2E07AAPT84251

Combo2E08CaucY2

Combo2E09CaucY10

Combo2E10AAY19

Combo2E11HispY27

Combo2E12AAY35


Combo2F02CaucTT50697


Combo2F04AsianUT57635

Combo2F05AATT50916

Combo2F06AAPT84209

Combo2F07AAPT84252

Combo2F08CaucY3

Combo2F09CaucY12

Combo2F10HispY20

Combo2F11HispY28

Combo2F12AAY36


Combo2G02CaucTT50698


Combo2G04AsianOT06795

Combo2G05AATT50922

Combo2G06AAPT84210

Combo2G07AAPT84253

Combo2G08CaucY4

Combo2G09AAY13

Combo2G10HispY21

Combo2G11HispY29

Combo2G12AAY37


Combo2H02CaucTT50700


Combo2H04AsianPC16856

Combo2H05AATT50923

Combo2H06AAPT84211

Combo2H07AAPT84254

Combo2H08CaucY5

Combo2H09AAY14

Combo2H10HispY22

Combo2H11HispY30

Combo2H12HispY38

Analysis-AFDIL

Variant listName of ProfileSampleHaplogroupMissing MutationsPrivate MutationsContinentRegion

C1B01CaucGT38086263G 315.1C 477C 750G 1438G 3010A 4767G 4769G 8860G 15326G 16189C 16519CH1c21GT38086H1c21noneT16189CEurope (H)

C1C01CaucGT3808773G 146C 263G 309.1C 309.2C 315.1C 458T 709A 750G 930A 1438G 1709A 1888A 2706G 4216C 4769G 4917G 5147A 7028T 8697A 8730G...T2b6bGT38087T2b6bnonenoneEuropeSpain

C1D01CaucGT3808973G 185A 228A 263G 295T 309.1C 315.1C 462T 489C 750G 1438G 2706G 3010A 4216C 4769G 7028T 8860G 10084C 11251G 11719A 1261...J1c8aGT38089J1c8anoneT16189CEuropePoland, Germany, Serbia, Uzbekistan

C1E01CaucGT3809172C 263G 309.1C 315.1C 750G 1438G 2706G 4580A 4769G 7028T 8860G 10933T 15326G 15467G 15904T 16298CEuropeGT38091VnoneC10933T A15467GEuropeSpain, Slovakia, Hungary

C1F01CaucGT38092198T 263G 315.1C 456T 524.1A 524.2C 524.3A 524.4C 722T 750G 1438G 4769G 8343G 8860G 9327G 12771A 13434G 13801G 15326G 15...H5e1a1GT38092H5e1a1noneC198T A9327G A13801G T15670CEurope (H)

C1G01CaucGT38093150T 263G 315.1C 750G 1438G 3010A 4769G 8349T 8860G 14053G 15326G 16355T 16519C>JQ702360.1GT38093H1ononenoneEuropePortugal

C1H01CaucGT38094263G 309.1C 315.1C 750G 1438G 4502C 4769G 8860G 9948A 11252G 15326G 15784C 16519C>HM625709.1GT38094H65noneA11252GEurope (H)

C1A02CaucGT3809573G 199C 203A 204C 250C 263G 309.1C 315.1C 455.1T 709A 750G 1438G 1719A 2706G 3447G 3990T 4529T 4769G 6734A 7028T 8251A ...I1a1bGT38095I1a1b-573.1C G709A C9727TEurope (I1a1)

C1B02CaucGT3809773G 114T 263G 315.1C 497T 750G 1189C 1438G 1811G 2706G 3480G 4769G 7028T 8027A 8860G 9055A 9698C 10398G 10550G 11299C 11...K1a1b1GT38097K1a1b1noneG8027A G15301AEuropeSlovakia, Hungary

C1C02CaucGT38098152C 263G 315.1C 523del 524del 750G 1438G 3010A 3796G 4769G 8860G 15326G 15519A 16111T 16189C 16356C 16519C>JQ704003.1GT38098H1b1A16183C -309.1C -309.2C C16111T T152CEuropeGermany, Romania

C1D02CaucGT38100263G 309.1C 315.1C 750G 1438G 3010A 4655A 4769G 8860G 12354C 15326G 16189C 16519C>JQ704300.1GT38100H1none-309.1C G4655AEuropeSpain, Germany, Poland, Romania

C1E02CaucGT38106263G 309.1C 315.1C 2416C 8817GH2a2aGT38106H2a2anoneT2416C A8817GEuropeSpain

C1F02CaucGT3810773G 263G 309.1C 315.1C 750G 1438G 1700C 2706G 3197C 3388A 4769G 5495C 7028T 8788T 8860G 9477A 11467G 11719A 12308G 12372...U5a1a1GT38107U5a1a1noneC3388A C8788TEuropeSpain, Romania, Serbia

C1G02CaucGT38108263G 309.1C 309.2C 315.1C 750G 1438G 3010A 4373C 4769G 8860G 15313C 15326G 16189C 16519CH1+16189GT38108H1+16189noneT4373C T15313CEuropeAll areas

C1H02CaucJA4432773G 152C 199C 204C 207A 250C 263G 315.1C 750G 1438G 1719A 2706G 4529T 4769G 7028T 8251A 8860G 10034C 10238C 10398G 11719...I2JA44327I2-573.1C G16474TEurope (I)

C1A03CaucJM2831573G 146C 152C 263G 315.1C 709A 750G 1438G 1811G 2706G 3480G 4561C 4769G 7028T 8860G 9055A 9698C 9716C 10550G 11299C 1146...>JQ705301.1JM28315K2a6-309.1C noneEuropeSpain

C1B03CaucJT5234573G 263G 309.1C 315.1C 456T 523del 524del 750G 1438G 2851G 4095T 4336C 4769G 8860G 9055A 13194A 15326G 15833T 16138G 163...H5a1c1aJT52345H5a1c1anoneA16138G A73GEuropeCentral and Eastern

C1C03CaucJT52346146C 263G 309.1C 309.2C 315.1C 456T 750G 1438G 4769G 8860G 15326G 16292T 16304C 16325C>JQ702019.1JT52346H5gnonenoneEuropeSpain

C1D03CaucMT9712173G 185A 188G 228A 263G 295T 309.1C 315.1C 462T 489C 750G 1438G 2706G 3010A 4216C 4769G 7028T 7762A 8860G 10398G 11251G ...J1c2MT97121J1c2noneT16093C G7762AEuropeRomania

C1E03CaucMT9712273G 152C 263G 315.1C 709A 750G 930A 1438G 1888A 2706G 4216C 4769G 4917G 5147A 7028T 8697A 8860G 10463C 11242G 11251G 117...>EU683970.1MT97122T2b2bnonenoneEuropeBulgaria, Serbia

C1F03CaucMT9712373G 152C 195C 263G 315.1C 709A 750G 1438G 1888A 2706G 4216C 4769G 4917G 7028T 8697A 8860G 9899C 10463C 11251G 11719A 126...T1a1MT97123T1a1noneA16158GEurope (T1a)

C1G03CaucMT9712473G 263G 309.1C 315.1C 497T 524.1A 524.2C 524.3A 524.4C 750G 1189C 1438G 1811G 2706G 3480G 4769G 4961G 7028T 7337A 8860G...>JQ705445.1MT97124K1aT16093C -309.1C -524.3A -524.4CEuropeSlovakia

C1H03CaucMT9712573G 152C 263G 309.1C 315.1C 523del 524del 750G 1438G 2706G 3197C 3750T 4769G 7028T 7843G 7978T 8104C 8860G 9148C 9477A 1...U5a2d1aMT97125U5a2d1anoneT152CEurope (U5a)All areas

C1A04CaucMT9712673G 150T 263G 309.1C 315.1C 750G 1438G 1811G 2294G 2706G 3010A 4703C 4769G 6518T 7028T 8860G 9266A 10506G 11467G 11719A ...U3a1cMT97126U3a1cnoneT16342C

C1B04CaucMT9713173G 228A 263G 295T 315.1C 462T 482C 489C 750G 1438G 2706G 3010A 3394C 4216C 4769G 7028T 8860G 9635C 10398G 11116C 11251G...J1c1aMT97131J1c1anoneT11116C C12346T

C1C04CaucMT9713616T 73G 150T 199C 263G 309.1C 315.1C 497T 750G 1189C 1438G 1811G 2706G 3480G 4769G 7028T 7519del 8281del 8282del 8283del...K1a11bMT97136K1a11bnoneA16215G A7519-

C1D04CaucMT9713973G 150T 152C 195C 215G 263G 295T 310.1T 315.1C 319C 489C 513A 750G 1438G 1850C 2706G 3447G 4216C 4769G 6731C 7028T 7476...J2a1a1a2MT97139J2a1a1a2noneT6731C

C1E04CaucMT9714173G 146C 153G 195C 225A 226C 263G 315.1C 524.1A 524.2C 750G 1438G 1719A 2706G 4769G 6221C 6371T 7028T 8393T 8425G 8860G ...>JQ702482.1MT97141X2b+226-309.1C -524.1A -524.2C

C1F04CaucMT9714573G 152C 195C 263G 315.1C 499A 524.1A 524.2C 750G 961C 1438G 1811G 2706G 4646C 4769G 5999C 6047G 7028T 8818T 8860G 11332...U4a1aMT97145U4a1anonenone

C1G04CaucMT97150146C 263G 309.1C 309.2C 315.1C 456T 750G 1438G 4336C 4769G 8860G 9053A 15326G 15833T 16304C 16311C>JQ705315.1MT97150H5a1noneT146C -309.2C

C1H04CaucMT97152263G 309.1C 315.1C 750G 1438G 4769G 6776C 8084T 8860G 15326G 16519C>JQ702808.1MT97152H3nonenone

C1A05CaucMT9715573G 263G 309.1C 315.1C 524.1A 524.2C 709A 750G 960.1C 1438G 1888A 2706G 2850C 4216C 4769G 4917G 6632C 7022C 7028T 8697A ...>AY495304.1MT97155T2a1anone-524.1A -524.2C -960.1C

C1B05CaucMT9715673G 152C 195C 198T 263G 309.1C 315.1C 709A 750G 1438G 1888A 2706G 4216C 4769G 4917G 7028T 7870C 8697A 8860G 9899C 10463C...T1a1MT97156T1a1noneC198T T7870C

C1C05CaucMT9715873G 152C 195C 263G 309.1C 315.1C 709A 750G 1438G 1888A 2706G 4216C 4769G 4917G 7028T 8697A 8860G 9899C 10463C 11251G 117...T1a1MT97158T1a1nonenone

C1D05CaucMT97159263G 309.1C 315.1C 750G 1438G 2259T 4745G 4769G 8860G 13680T 14560A 14872T 15326G 16129A>AY495149.1MT97159H13a1anonenone

C1E05CaucPT86478263G 309.1C 315.1C 750G 1438G 3010A 4769G 5460A 7711C 8860G 12070A 15326G 15817G 16519CH1e2aPT86478H1e2anoneT7711C

C1F05CaucTT51669263G 309.1C 309.2C 315.1C 477C 750G 1438G 3010A 4769G 5318T 8860G 12858T 15326G 16519CH1c2TT51669H1c2noneC5318T

C1G05CaucTT5167573G 263G 315.1C 750G 1438G 2706G 3197C 4769G 7028T 8860G 9477A 9667G 11467G 11719A 12308G 12372A 13617C 14766T 14793G 15...U5a1b1TT51675U5a1b1nonenone

C1H05CaucTT51676263G 309.1C 315.1C 456T 750G 1438G 3666A 4769G 5302C 8860G 15326G 16304C 16311C 16391A>JQ703266.1TT51676H5snonenone

C1A06CaucTT51677263G 309.1C 309.2C 315.1C 750G 1438G 4769G 8860G 13830C 14470A 15326G 16093C 16124C 16221T 16519C>JQ703002.1TT51677H10e1nonenone

C1B06CaucTT5167973G 263G 315.1C 709A 750G 1438G 1888A 2706G 2850C 4216C 4769G 4917G 7022C 7028T 8697A 8860G 10463C 11251G 11719A 11812G ...T2a1aTT51679T2a1anonenone

C1C06CaucTT5168072C 73G 152C 263G 315.1C 537T 750G 1438G 2706G 4580A 4769G 7028T 8860G 13105G 14770T 15326G 15904T 16086C 16298CV2bTT51680V2bnoneT16086C A73G T152C C537T

C1D06CaucTT5168273G 150T 152C 195C 215G 263G 295T 310.1T 315.1C 319C 489C 513A 750G 1438G 1850C 2706G 3447G 4216C 4769G 7028T 7476T 7789...J2a1a1a2TT51682J2a1a1a2C16261T none

C1E06CaucTT5168373G 151T 263G 309.1C 315.1C 709A 750G 930A 1438G 1888A 2706G 4216C 4769G 4917G 5147A 7028T 8697A 8860G 9809G 10463C 1075...>JQ702951.1TT51683T2b3enonenone

C1F06CaucTT51684263G 309.1C 315.1C 523del 524del 750G 1438G 3010A 4769G 8860G 15314A 15326G 15924G 16519C>HM000002.1TT51684H1+16311T16311C none

C1G06CaucTT5168573G 143A 153G 195C 200G 263G 309.1C 315.1C 750G 1438G 1719A 2706G 3552C 4769G 6221C 6371T 6680C 7028T 7299G 8422G 8860G ...X2a1b1aTT51685X2a1b1anonenone

C1H06CaucUT58303143A 263G 315.1C 750G 1438G 3010A 3666A 4769G 5393C 5899.1C 8860G 15326G 16239A 16519CH1ak1UT58303H1ak1noneC16239A G143A -5899.1C

Group 49to96

C1H08CaucGC03394152C 263G 309.1C 315.1C 750G 1438G 1809C 4769G 8718G 8860G 9299G 15326G 16519CH86H86noneT152C A8718G A9299GEurope (H)

C1A09CaucGT36864Not analyzed on first pass

C1B09CaucGT3686673G 210G 263G 309.1C 315.1C 750G 1438G 3010A 4769G 6365C 8860G 15326G 16162G 16209C 16278T 16519CH1a1H1a1noneC16278T A210GEuropeRomania

C1C09CaucGT3687573G 152C 195C 263G 309.1C 315.1C 499A 750G 73G 152C 263G 315.1C 709A 750G 1438G 1888A 2706G 4216C 4769G 4904T 4917G 5964...T1a5T1a5A16163G T16093C A16399G T152C C4904T T5964C A10502G T11569CEuropeRomania

C1D09CaucGT36877263G 315.1C 456T 523del 524del 750G 1438G 4336C 4769G 8860G 11719A 15326G 15833T 16304CH5a1bH5a1bnonenoneEurope (H)Germany, Poland

C1E09CaucGT36878152C 263G 315.1C 750G 1438G 4769G 8860G 10394T 14155T 14869C 15326G 16519CH16dH16dnonenoneEurope (H)

C1F09CaucGT3688473G 150T 152C 195C 215G 263G 295T 310.1T 315.1C 319C 489C 513A 750G 1438G 1850C 2706G 3447G 4216C 4769G 7028T 7476T 7789..J2a1a1a2J2a1a1a2nonenone

C1G09CaucGT3688573G 152C 195C 263G 309.1C 315.1C 499A 750G 73G 152C 185A 263G 295T 315.1C 462T 489C 750G 1438G 2706G 3010A 4216C 4769G 7...J1c3bJ1c3bnoneT152C T195C G499A

C1H09CaucGT3688673G 152C 195C 263G 309.1C 315.1C 499A 750G 1438G 1811G 2706G 4646C 4769G 5999C 6047G 7028T 8155A 8818T 8860G 11332T 1146...U4a1cU4a1cnonenone

C1D07CaucGT3806573G 152C 195C 263G 309.1C 315.1C 499A 750G 73G 152C 263G 315.1C 709A 750G 1438G 1888A 73G 195C 263G 315.1C 523del 524del...>JQ705993.1H1a3bnoneA16241C T152C -309.1C G499A G709A G1888A

C1E07CaucGT3806673G 152C 195C 263G 309.1C 315.1C 499A 750G 73G 152C 195C 263G 309.1C 315.1C 709A 750G 1438G 1888A 2706G 4216C 4769G 4917...T1a1T1a1noneG499A

C1F07CaucGT3806773G 143A 189G 192C 194T 195C 207A 263G 309.1C 315.1C 489C 709A 750G 1243C 1438G 2706G 3505G 4769G 5046A 5460A 7028T 8251...W9W9T204C G143A T192C T489C

C1G07CaucGT38069263G 315.1C 524.1A 524.2C 750G 1438G 4769G 4793G 8860G 15326G 16355T 16519C>JQ705594.1H7none-524.1A -524.2C

C1H07CaucGT38070263G 309.1C 315.1C 750G 1438G 2706G 4769G 7028T 8860G 9801A 10205T 10920T 15326G 15514C 16311C>HQ384193.1HV+16311nonenone

C1A08CaucGT38072Not analyzed on first pass

C1B08CaucGT3807373G 146C 195C 263G 310C 315del 499A 524.1A 524.2C 750G 1438G 1811G 2706G 4646C 4769G 5999C 6047G 7028T 8818T 8860G 10172...U4a2U4a2noneT146C C315- G10172A

C1C08CaucGT38075263G 315.1C 750G 1438G 4769G 4793G 8860G 15326G 16355T 16519C>JQ705594.1H7nonenone

C1D08CaucGT3807673G 185A 189G 203A 204C 263G 309.1C 315.1C 750G 1438G 1700C 2706G 3197C 4769G 5495C 7028T 8860G 9477A 11467G 11719A 1230...>JQ705318.1U5a1a1dnoneG203A

C1E08CaucGT38078263G 315.1C 750G 1438G 4769G 8860G 10394T 11887A 15043A 15326G 16519CH16H16noneG11887A G15043A

C1F08CaucGT38081263G 309.1C 315.1C 750G 1438G 2706G 4580A 4769G 7028T 8860G 10609C 12810G 15181G 15326G 15904T 16216G 16298CV3cV3cT72C T10609C A15181G

C1G08CaucGT38083196C 263G 309.1C 315.1C 750G 1438G 4769G 8860G 9545G 11152C 12651A 13500C 14203G 15326G 16519CH26a1a1H26a1a1nonenone

C1A10CaucJT51178263G 293C 315.1C 750G 1438G 4769G 6776C 8860G 8937C 12346T 15326G 15530C 16209C 16519C>JQ703690.1H3z1nonenone

C1B10CaucJT5121173G 263G 315.1C 750G 1438G 2706G 3348G 3969T 4172A 4769G 7028T 7805A 8754T 8860G 11467G 11719A 11938T 12308G 12372A 1370...>JQ702612.1U6a1a1-309.1C none

C1C10CaucMT9480373G 263G 309.1C 315.1C 750G 1438G 3010A 4769G 6365C 8860G 15326G 16162G 16209C 16519CH1a1H1a1nonenone

C1D10CaucMT9480773G 152C 195C 263G 309.1C 315.1C 709A 750G 1438G 1888A 2706G 4216C 4769G 4917G 7028T 8697A 8860G 9120G 9899C 10463C 1125...>JQ703894.1T1a1cnonenone

C1E10CaucMT94815152C 263G 309.1C 315.1C 709A 750G 1438G 3010A 4769G 8200C 8860G 9101C 15326G 16519CH30b1H30b1nonenone

C1F10CaucMT9481773G 152C 199C 204C 263G 315.1C 669C 750G 1438G 1719A 2702A 2706G 3336C 4769G 5315G 7028T 8860G 8901G 10238C 10398G 10598...>JQ704871.1N1a1a1a3-573.1C -573.2C -573.3C none

C1G10CaucMT94818263G 309.1C 315.1C 750G 1193C 1438G 2706G 4204C 4769G 5581G 7028T 8860G 12492T 12599C 15326G 16311C 16519C>JQ702536.1HV16nonenone

C1H10CaucMT9482673G 242T 263G 295T 309.1C 315.1C 462T 489C 750G 1438G 2158C 2706G 3010A 4216C 4769G 5460A 5463T 6911C 7028T 8269A 8557A ...>HQ286325.1J1b1a1aG16390A none

C1A11CaucMT94827146C 195C 263G 315.1C 750G 961G 1438G 4769G 7278C 8227C 8448C 8860G 13759A 15326G 16293G 16311C>JQ703593.1H11anonenone

C1B11CaucMT94829146C 195C 249del 263G 309.1C 315.1C 750G 961G 1438G 4769G 8448C 8860G 8898T 13759A 15326G 16278T 16293G 16311C>GU122994.1H11a1noneA249- -309.1C

C1C11CaucMT9483173G 263G 309.1C 315.1C 497T 524.1A 524.2C 750G 1189C 1438G 1811G 2706G 3480G 4769G 5773A 7028T 8860G 9055A 9698C 10398G ...K1a2aK1a2anoneG16145A T10786C

C1D11CaucMT9483373G 152C 263G 315.1C 533G 709A 750G 1438G 1842G 1888A 2695A 2706G 4216C 4769G 4917G 6261A 7028T 8455T 8697A 8860G 10463C...T2c1aT2c1a-573.1C T16172C C16266T T152C A533G A1842G G2695A C13770T G13928C

C1E11CaucMT9483473G 263G 315.1C 709A 750G 930A 1438G 1888A 2706G 4216C 4769G 4917G 5147A 7028T 8697A 8860G 10463C 11251G 11719A 11812G 1...T2bT2bnoneT13488C

C1F11CaucMT9483573G 146C 242T 263G 295T 309.1C 315.1C 462T 489C 750G 1438G 2158C 2706G 3010A 4216C 4769G 5460A 7028T 8269A 8557A 8860G 1...>JQ704626.1J1b1a1nonenone

C1G11CaucMT94838263G 593C 750G 1438G 4769G 6296T 14869A 15326G 16129A 16519C>AY495154.1H17a2-309.1C -315.1C G3915A A8860G none

C1H11CaucMT9483973G 228A 234G 263G 315.1C 709A 750G 930A 1438G 1888A 2706G 4216C 4769G 4917G 5147A 7028T 8697A 8860G 10463C 11251G 11719...>HM055613.1T2b-309.1C A234G G11914A

C1A12CaucMT94842263G 309.1C 315.1C 750G 1438G 3010A 4769G 8860G 15326G 16189C 16356C 16519CH1bH1bnonenone

C1B12CaucMT9484373G 152C 217C 263G 309.1C 315.1C 340T 508G 523del 524del 750G 1438G 1811G 2526T 2706G 3720G 4769G 5390G 5426C 6045T 6152...>EF452294.1U2e1enonenone

C1C12CaucMT9484654.1C 56C 93G 263G 309.1C 315.1C 573.1C 573.2C 750G 1438G 4769G 6253C 8860G 11410C 14953T 15326GH15a1H15a1T55C T57C -54.1C A56C A93G -573.1C -573.2C

C1D12CaucMT94848152C 195C 257G 263G 309.1C 309.2C 315.1C 477C 750G 1438G 3010A 3172T 4769G 8473C 8860G 15326G 16519C>HM625701.1H1c3none-309.2C C3172T

C1E12CaucMT94850263G 309.1C 309.2C 315.1C 750G 1438G 3010A 4769G 8860G 15326G 16189C 16298C 16519C>HQ659690.1H1+16189nonenone

C1F12CaucMT9485373G 263G 309.1C 315.1C 321C 709A 750G 1438G 1888A 2706G 4216C 4769G 4917G 5147A 5426C 6137C 7028T 8572A 8697A 8860G 1046...T2b24aT2b24aG930A T16445C T6137C

C1G12CaucMT9485573G 143A 189G 192C 194T 195C 196C 204C 207A 263G 315.1C 709A 750G 1243C 1438G 2706G 3505G 3531A 4769G 5046A 5460A 7028T ...W4a1W4a1nonenone

C1H12CaucMT9485873G 152C 263G 309.1C 315.1C 523del 524del 750G 921C 1438G 2706G 3203G 4659A 4769G 5147A 5372G 6680C 7028T 7424G 8618C 87...L3d1c1L3d1c1noneG4659A

C1A07CaucUT5830573G 151T 152C 263G 309.1C 315.1C 709A 750G 930A 1438G 1888A 2706G 4216C 4769G 4917G 5147A 7028T 8697A 8860G 10463C 10750...T2b3+151T2b3+151noneT16311C G16390A T152C T11253C

C1B07CaucUT5831073G 185A 188G 228A 263G 295T 309.1C 315.1C 462T 489C 523del 524del 750G 1438G 2706G 3010A 4216C 4769G 6620C 7028T 8860G ...J1c2dJ1c2dnonenone

C1C07CaucZT8138273G 185A 188G 228A 263G 295T 309.1C 315.1C 263G 315.1C 456T 750G 1438G 2626C 4769G 7424G 8020A 8860G 11161T 15326G 16304...H5kH5knoneA73G G185A A188G G228A C295T A7424G C11161T

https://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypes

Sheet2

SampleMissing MutationsPrivate MutationsHaplogroupContinent

GT38086noneT16189CH1c21Europe (H)

GT38087nonenoneT2b6bEurope

GT38089noneT16189CJ1c8aEurope

GT38091noneC10933T A15467GVEurope

GT38092noneC198T A9327G A13801G T15670CH5e1a1Europe (H)

GT38093nonenoneH1oEurope

GT38094noneA11252GH65Europe (H)

GT38095-573.1C G709A C9727TI1a1bEurope (I1a1)

GT38097noneG8027A G15301AK1a1b1Europe

GT38098A16183C -309.1C -309.2C C16111T T152CH1b1Europe

GT38100none-309.1C G4655AH1Europe

GT38106noneT2416C A8817GH2a2aEurope

GT38107noneC3388A C8788TU5a1a1Europe

GT38108noneT4373C T15313CH1+16189Europe

JA44327-573.1C G16474TI2Europe (I)

JM28315-309.1C noneK2a6Europe

JT52345noneA16138G A73GH5a1c1aEurope

JT52346nonenoneH5gEurope

MT97121noneT16093C G7762AJ1c2Europe

MT97122nonenoneT2b2bEurope

MT97123noneA16158GT1a1Europe (T1a)

MT97124T16093C -309.1C -524.3A -524.4CK1aEurope

MT97125noneT152CU5a2d1aEurope (U5a)

https://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypes

AnalysisQ25-ILMN

GM Excess HP CallsGM Missed VariantsCommentComment2

Group 1to48Matches in DBSourceName of ProfileHaplogroupMissing MutationsPrivate MutationsQuery

C1B01CaucGT38086PhylotreeH1c21H1c21noneT16189C263G 309.1C 315.1C 477C 750G 1438G 3010A 4767G 4769G 8860G 15326G 16189C 16519C

C1C01CaucGT38087PhylotreeT2b6bT2b6bnonenone73G 146C 263G 309.1C 309.2C 315.1C 458T 709A 750G 930A 1438G 1709A 1888A 2706G 4216C 4769G 4917G 5147A 7028T 8697A 8730G...

C1D01CaucGT38089PhylotreeJ1c8aJ1c8anoneT16189C73G 185A 228A 263G 295T 309.1C 315.1C 462T 489C 750G 1438G 2706G 3010A 4216C 4769G 7028T 8860G 10084C 11251G 11719A 1261...

C1E01CaucGT38091PhylotreeVVnoneC10933T A15467G72C 263G 309.1C 315.1C 750G 1438G 2706G 4580A 4769G 7028T 8860G 10933T 15326G 15467G 15904T 16298C

C1F01CaucGT38092PhylotreeH5e1a1H5e1a1noneC198T A9327G A13801G T15670C198T 263G 315.1C 456T 524.1A 524.2C 524.3A 524.4C 722T 750G 1438G 4769G 8343G 8860G 9327G 12771A 13434G 13801G 15326G 15...

C1G01CaucGT38093GenBank>JQ702360.1H1ononenone150T 263G 315.1C 750G 1438G 3010A 4769G 8349T 8860G 14053G 15326G 16355T 16519C

C1H01CaucGT38094PhylotreeH65H65noneG9948A A11252G263G 309.1C 315.1C 750G 1438G 4769G 8860G 9948A 11252G 15326G 15784C 16519C

C1A02CaucGT38095PhylotreeI1a1bI1a1b-573.1CG709A C9727T73G 199C 203A 204C 250C 263G 309.1C 315.1C 455.1T 709A 750G 1438G 1719A 2706G 3447G 3990T 4529T 4769G 6734A 7028T 8251A ...

C1B02CaucGT38097PhylotreeK1a1b1K1a1b1noneG8027A G15301A73G 114T 263G 315.1C 497T 750G 1189C 1438G 1811G 2706G 3480G 4769G 7028T 8027A 8860G 9055A 9698C 10398G 10550G 11299C 11...

C1C02CaucGT38098Missing regions - insufficient quality?GenBank>JQ704003.1H1b1A16183C -309.1C -309.2CC16111T T152C152C 263G 315.1C 523del 524del 750G 1438G 3010A 3796G 4769G 8860G 15326G 15519A 16111T 16189C 16356C 16519C

C1D02CaucGT38100GenBank>JQ704300.1H1none-309.1C G4655A263G 309.1C 315.1C 750G 1438G 3010A 4655A 4769G 8860G 12354C 15326G 16189C 16519C

C1E02CaucGT38106PhylotreeH2a2aH2a2anoneT2416C A8817G263G 309.1C 315.1C 2416C 8817G

C1F02CaucGT38107PhylotreeU5a1a1U5a1a1noneC3388A C8788T73G 263G 309.1C 315.1C 750G 1438G 1700C 2706G 3197C 3388A 4769G 5495C 7028T 8788T 8860G 9477A 11467G 11719A 12308G 12372...

C1G02CaucGT38108GenBank>JQ704557.1H1+16239C16239T T152C -309.1CT4373C A10840G263G 315.1C 750G 1438G 3010A 4373C 4769G 8860G 10840G 15313C 15326G 16519C

C1H02CaucJA44327Appears to be 1:1 mixture with some shared variantsrerunPhylotreeI2I2G16129A T199C -573.1C G1719A A2706G A4529T C7028T G8251Anone73G 152C 204C 207A 250C 263G 315.1C 750G 1438G 4769G 8860G 10034C 10238C 10398G 11719A 12501A 12705T 13780G 14766T 15043...

C1A03CaucJM28315GenBank>JQ705301.1K2a6-309.1Cnone73G 146C 152C 263G 315.1C 709A 750G 1438G 1811G 2706G 3480G 4561C 4769G 7028T 8860G 9055A 9698C 9716C 10550G 11299C 1146...

C1B03CaucJT52345PhylotreeH5a1c1aH5a1c1anoneA16138G A73G73G 263G 309.1C 315.1C 456T 523del 524del 750G 1438G 2851G 4095T 4336C 4769G 8860G 9055A 13194A 15326G 15833T 16138G 163...

C1C03CaucJT52346GenBank>JQ702019.1H5gnonenone146C 263G 309.1C 309.2C 315.1C 456T 750G 1438G 4769G 8860G 15326G 16292T 16304C 16325C

C1D03CaucMT97121Missing coverage in region 13669-13758 (Amp1 low)PhylotreeJ1c2J1c2G13708AT16093C G7762A73G 185A 188G 228A 263G 295T 309.1C 315.1C 462T 489C 750G 1438G 2706G 3010A 4216C 4769G 7028T 7762A 8860G 10398G 11251G ...

C1E03CaucMT97122GenBank>EU683970.1T2b2bnonenone73G 152C 263G 315.1C 709A 750G 930A 1438G 1888A 2706G 4216C 4769G 4917G 5147A 7028T 8697A 8860G 10463C 11242G 11251G 117...

C1F03CaucMT97123Possible 80/20 mixturererunPhylotreeT1a1T1a1noneA16158G73G 152C 195C 263G 315.1C 709A 750G 1438G 1888A 2706G 4216C 4769G 4917G 7028T 8697A 8860G 9899C 10463C 11251G 11719A 126...

C1G03CaucMT97124PhylotreeK1aK1aA2706G A3480G C7028T G9055AC16256T T15479C73G 263G 309.1C 315.1C 497T 524.1A 524.2C 524.3A 524.4C 750G 1189C 1438G 1811G 4769G 8860G 9698C 10398G 10550G 11299C 11...

C1H03CaucMT97125Possible 30.70 mixturererunPhylotreeU5a2U5a2C16192T T3197C G9477AT152C A4529T G8251A C11107T T14577G73G 152C 263G 309.1C 315.1C 523del 524del 750G 1438G 2706G 4529T 4769G 7028T 8251A 8860G 11107T 11467G 11719A 12308G 123...

C1A04CaucMT97126PhylotreeU3a1cU3a1cnoneT16342C73G 150T 263G 309.1C 315.1C 750G 1438G 1811G 2294G 2706G 3010A 4703C 4769G 6518T 7028T 8860G 9266A 10506G 11467G 11719A ...

C1B04CaucMT97131PhylotreeJ1c1aJ1c1anoneT11116C C12346T73G 228A 263G 295T 315.1C 462T 482C 489C 750G 1438G 2706G 3010A 3394C 4216C 4769G 7028T 8860G 9635C 10398G 11116C 11251G...

C1C04CaucMT97136Some difficulty with CCCCTCT at position 8280 (heteroplasmic for deletion at 8281-8290?)OKPhylotreeK1a11bK1a11bnoneA16215G A7519-16T 73G 150T 199C 263G 309.1C 315.1C 497T 750G 1189C 1438G 1811G 2706G 3480G 4769G 7028T 7519del 8281del 8282del 8283del...

C1D04CaucMT97139PhylotreeJ2a1a1a2J2a1a1a2noneT6731C73G 150T 152C 195C 215G 263G 295T 310.1T 315.1C 319C 489C 513A 750G 1438G 1850C 2706G 3447G 4216C 4769G 6731C 7028T 7476...

C1E04CaucMT97141GenBank>JQ702482.1X2b+226A16183C T16189C C16223T -309.1C-524.1A -524.2C73G 146C 153G 195C 225A 226C 263G 315.1C 524.1A 524.2C 750G 1438G 1719A 2706G 4769G 6221C 6371T 7028T 8393T 8425G 8860G ...

C1F04CaucMT97145PhylotreeU4a1aU4a1anonenone73G 152C 195C 263G 315.1C 499A 524.1A 524.2C 750G 961C 1438G 1811G 2706G 4646C 4769G 5999C 6047G 7028T 8818T 8860G 11332...

C1G04CaucMT97150GenBank>JQ705315.1H5a1noneT146C -309.2C146C 263G 309.1C 309.2C 315.1C 456T 750G 1438G 4336C 4769G 8860G 9053A 15326G 15833T 16304C 16311C

C1H04CaucMT97152Possible 12% contaminantrerun?PhylotreeHHnonenone263G 309.1C 315.1C 750G 1438G 4769G 8860G 15326G 16519C

C1A05CaucMT97155

C1B05CaucMT97156Many HP in 2-3% range from 9900 through1 to ~700 possible Amplicon1 contaminantrerun?

C1C05CaucMT97158Low coverage from nt 2000 to 9000. No gaps. Possible 5% contaminant in Amplicon 1.Rerun?

C1D05CaucMT97159Good

C1E05CaucPT86478Good

C1F05CaucTT51669Good

C1G05CaucTT51675

C1H05CaucTT51676

C1A06CaucTT51677

C1B06CaucTT51679

C1C06CaucTT51680

C1D06CaucTT51682

C1E06CaucTT51683

C1F06CaucTT51684

C1G06CaucTT51685

C1H06CaucUT58303

Follow-up QC

Analyzed at Q40 and 99% IDAnalyzed at Q35 and 99% ID

C1 plate Amp1 failures

A05MT97155

A07UT58305

B05MT97156

B06TT51679

C01GT38087Min Cov: 11 Max Cov: 6958 Avg Cov: 2410Low coverage from ~ 1,800 to 9,500 (~1000 x) but seems to be complete genome. Position 301-322 appears to be very low coverage. No reads in HV2 C-stretch.

C05MT97158

C09GT36875

C10MT94803some yield

D10MT94807

D11MT94833

E03MT97122

E06TT51683

E07GT38066

E11MT94834

F03MT97123

F12MT94853

G11MT94838

H11MT94839

C1 plate Amp2 failures

A10JT51178

A11MT94827

B09GT36866some yield

C02GT38098Low coverage in Amp2 region, some regions of N's.

D01GT38089Low coverage in Amp2 region, some regions of N's. HV2 C-stretch not covered.

D03MT97121

E01GT38091Low coverage in Amp2 region, one region of N's 13,635 - 13,774. HV2 C-stretch not covered.

F01GT38092Good coverage across genome. May have been quantitation failure. HV2 C-stretch not covered.

G01GT38093Good coverage across genome. May have been quantitation failure. HV2 C-stretch not covered.

G02GT38108

G03MT97124

C1 plate failed both Amp 1&2

G11MT94838

Concordance data

Sample NameSelf ID EthnicityForenSeq-Kidd55 Ancestry SNP ConflictsmitoHg

Peter M. Vallone: Peter M. Vallone:Assigned by Coble or Jodi IrwinGeographical Mito (Coble)Y-HgGeo Y General grouping (de Knijff)refnumberPlatePositionEthnicityNameY-haplogroup (nomenclature Karafet 2008)Haplogroup-E (nomenclature Karafet 2008)Y-haplogroup (nomenclature Jobling 2003)

AF51AAsianD4kAsiaDAsia (mainly Japan, China)X

AF52AAsianD/GAsiaDAsia (mainly Japan, China)X

AF55AAsianD/G (G)

Peter M. Vallone: Peter M. Vallone:Confirmned by Coble and Diegoli - additional mito sequencingAsiaDAsia (mainly Japan, China)X

AF56AAsianD/GAsiaOSouthern part of AsiaX

AF57AAsianF1bAsiaCAsiaX

AF58AAsianM7a1AsiaOSouthern part of AsiaX

AF59AAsianM (M10a)



AF61AAsianF1a1bAsiaDAsia (mainly Japan, China)X

AF62AAsianF1aAsiaOSouthern part of AsiaX

AF63AAsianD4a4AsiaOSouthern part of AsiaX

AF64AAsianD4e1a1AsiaOSouthern part of AsiaX

AF65AAsianN (N9)

Peter M. Vallone: Peter M. Vallone:Confirmned by Coble and Diegoli - additional mito sequencingEurasiaOSouthern part of AsiaX

AF66AAsianM35AsiaCAsiaX

AF67AAsianB5b1bAsiaOSouthern part of AsiaX


AF69AAsianF1b1AsiaOSouthern part of AsiaX


AF71AAsianM7b2AsiaOSouthern part of AsiaX

AF72AAsianM35AsiaOSouthern part of AsiaX

AF73AAsianB5bAsiaDAsia (mainly Japan, China)X


AF75AAsianM9aAsiaOSouthern part of AsiaX

AF76AAsianN9a1AsiaOSouthern part of AsiaX

AF77AAsianAAsiaDAsia (mainly Japan, China)X

AF78AAsianno datano dataERROR:#N/AX

AF79AAsianF1b1AsiaOSouthern part of AsiaX


AF81AAsianB4aAsiaDAsia (mainly Japan, China)X



AF86AAsianF2aAsiaOSouthern part of AsiaX

AF88AAsianD5bAsiaCAsiaX

AF89AAsianD4iAsiaDAsia (mainly Japan, China)X

AF90AAsianB4c1a1aAsiaDAsia (mainly Japan, China)X

AF91AAsianD4c1aincomplete CR dataOSouthern part of AsiaX

AF92AAsianB4c1cAsiaCAsiaX

AF93AAsianD/G (G)


AF94AAsianB5b1bAsiaOSouthern part of AsiaX

AF95AAsianM7b2AsiaDAsia (mainly Japan, China)X


AF97AAsianB4b1AsiaDAsia (mainly Japan, China)X


BC11352Caucno dataH1Mainly India442Combo1F03CaucBC11352H1n.o.a.H1ok

C51AAsianF1b1AsiaDAsia (mainly Japan, China)X

C52AAsianA5AsiaDAsia (mainly Japan, China)X

C53AAsianM7b2AsiaOSouthern part of AsiaX

GA05070HispA2AmericasQNative American605HispC12HispGA05070Q1an.o.a.Qok

GA05071HispA2AmericasR1b3Mainly western Europe582HispB01HispGA05071R1b1b2n.o.a.R1b3ok

GC03394CaucHEuropeJ2Middle Eastern region281C1H08CaucGC03394J2n.o.a.J2ok

GT36864CaucKEuropeIEurope198C1A09CaucGT36864In.o.a.Iok

GT36866CaucH1aEuropeJ2Middle Eastern region210C1B09CaucGT36866J2n.o.a.J2ok

GT36875CaucTEuropeR1b3Mainly western Europe222C1C09CaucGT3687

mtGenome Sequencing of NIST Reference Materials and ... · NIST Standard Reference Materials (SRMs)...

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