TB-Profiler result

Run: ERR2516580
Summary

Run ID: ERR2516580

Sample name:

Date: 31-03-2023 21:37:00

Number of reads: 1133939

Percentage reads mapped: 99.73

Strain: lineage4.6.2.2

Drug-resistance: MDR-TB

Download CSV Download TXT Download PDF Download JSON
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.6 Euro-American T;LAM None 1.0
lineage4.6.2 Euro-American T;LAM RD726 1.0
lineage4.6.2.2 Euro-American (Cameroon) LAM10-CAM RD726 0.99
Drug resistance-Associated Mutations: This table reports mutations found in candidate resistance genes which have been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
Non-Associated Mutations: This table reports mutations found in candidate resistance genes which have not been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
ccsA 620546 p.Leu219Pro missense_variant 0.22
rpoC 763031 c.-339T>C upstream_gene_variant 0.12
rpoC 766657 c.3288A>G synonymous_variant 0.18
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpR5 778298 c.-692C>T upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303644 c.714G>A synonymous_variant 0.11
Rv1258c 1407077 c.264C>T synonymous_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155389 c.723C>G synonymous_variant 1.0
PPE35 2169320 p.Leu431Phe missense_variant 0.2
Rv1979c 2221746 c.1416_1418dupCCG disruptive_inframe_insertion 0.94
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714616 c.717C>T synonymous_variant 0.11
pepQ 2859381 c.1038C>G synonymous_variant 0.2
thyX 3067474 p.Pro158Ala missense_variant 1.0
Rv3083 3448567 p.His22Asp missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612200 p.Val306Gly missense_variant 0.22
Rv3236c 3612571 c.546C>T synonymous_variant 1.0
panD 4044313 c.-32C>T upstream_gene_variant 0.11
embC 4239973 c.111T>G synonymous_variant 0.14
embC 4241339 p.Phe493Leu missense_variant 0.18
embA 4242550 c.-683C>G upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
aftB 4267272 p.Lys522Arg missense_variant 1.0
aftB 4269834 c.-998G>A upstream_gene_variant 0.17
ethA 4326624 p.Pro284Thr missense_variant 1.0
ethR 4326739 c.-810G>C upstream_gene_variant 1.0
ethA 4328004 c.-531C>T upstream_gene_variant 1.0
ethA 4328411 c.-938G>A upstream_gene_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0