Workshop on Whole Genome Sequencing and Analysis, 2-4 Oct. 2017

Recap Exercise 5

Filling out the metadata sheet

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

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

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