Recap Exercise 5 - GoSeqIt€¦ · like, catA1-like, dfrA1, mph(B), strA, strB, sul1, sul2, tet(A)...
Transcript of Recap Exercise 5 - GoSeqIt€¦ · like, catA1-like, dfrA1, mph(B), strA, strB, sul1, sul2, tet(A)...
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Workshop on Whole Genome Sequencing and Analysis, 2-4 Oct. 2017
Recap Exercise 5
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Filling out the metadata sheet
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ResultsSample Unknown_1 Unknown_2 Unknown_3
contigs 2 185 8
n50 4747819 168113 4918979
Species Escherichia coli query cov. = 97.11
Salmonella enterica query cov. = 98.18
Staphylococcus epidermidis query cov. = 33.23 (!)
MLST ST-135 ST-19 ST-8
Resistance genes
aadA1, blaTEM-1B-like, catA1-like, dfrA1, mph(B), strA, strB, sul1, sul2, tet(A)
aadA2, aadA5, strA, strB, aph(3')-Ic, aph(4)-Ia, aac(3)-Iva, armA, mph(E), sul1, dfrA1, tet(G), msr(E), floR, blaCARB-2, blaTEM-1B
blaZ-like, fosA, tet(K)
Plasmids IncQ1 IncX1, Col8282, ColRNAI
NA
Special
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ResultsSample Unknown_1 Unknown_2 Unknown_3contigs 2 185 8n50 4747819 168113 4918979Species Escherichia coli
Query cov. = 97.11Salmonella enterica Query cov. = 98.18
Staphylococcus epidermidis Query cov. = 33.23 (!)
MLST ST-135 ST-19 ST-8Resistance genes
aadA1, blaTEM-1B-like, catA1-like, dfrA1, mph(B), strA, strB, sul1, sul2, tet(A)
aadA2, aadA5, strA, strB, aph(3')-Ic, aph(4)-Ia, aac(3)-Iva, armA, mph(E), sul1, dfrA1, tet(G), msr(E), floR, blaCARB-2, blaTEM-1B
blaZ-like, fosA, tet(K)
Plasmids IncQ1 IncX1, Col8282, ColRNAI
NA
Special Rotavirus A Query cov. = Templ. cov. = 100
Aspergillus fumigatus Query cos. = 66.7
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ResultsGoSeqItToolsSample Unknown_1 Unknown_2 Unknown_3contigs 2 185 8n50 4747819 168113 4918979Species Escherichia coli
Query cov. = 97.11Salmonella enterica Query cov. = 98.18
Staphylococcus epidermidis Query cov. = 33.23 (!)
MLST ST-135 (E. coli #1) ST-19 ST-8Resistance genes
aadA1, blaTEM-1B-like, catA1-like, dfrA1, mph(B), strA, strB, sul1, sul2, tet(A)
aadA2, aadA5, strA, strB, aph(3')-Ic, aph(4)-Ia, aac(3)-Iva, armA, mph(E), sul1, dfrA1, tet(G), msr(E), floR, blaCARB-2, blaTEM-1B
blaZ-like, fosA, tet(K)
Plasmids IncQ1 IncX1, Col8282, ColRNAI
rep16, rep5, rep7, repUS14
Special ST64 (E. coli #2) NA NA