TB-Profiler result

Run: ERR017785
Summary

Run ID: ERR017785

Sample name:

Date: 31-03-2023 07:56:05

Number of reads: 2441349

Percentage reads mapped: 99.46

Strain: lineage4;lineage2.2.1

Drug-resistance: MDR-TB

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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
lineage2 East-Asian Beijing RD105 0.94
lineage4 Euro-American LAM;T;S;X;H None 0.13
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.92
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.94
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 0.91 rifampicin
rpoC 764841 p.Ile491Thr missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.84 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.21 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289252 c.-11A>C upstream_gene_variant 0.12 pyrazinamide
eis 2715342 c.-10G>A upstream_gene_variant 0.71 kanamycin
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
ethA 4326463 c.1010delT frameshift_variant 0.94 ethionamide, ethionamide
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
fgd1 491742 c.960T>C synonymous_variant 0.82
mshA 575907 p.Ala187Val missense_variant 0.86
ccsA 620625 p.Ile245Met missense_variant 0.95
rpoC 763031 c.-339T>C upstream_gene_variant 0.92
mmpL5 775639 p.Ile948Val missense_variant 0.92
mmpL5 776100 p.Thr794Ile missense_variant 0.87
mmpL5 776182 p.Asp767Asn missense_variant 0.9
mmpS5 779615 c.-710C>G upstream_gene_variant 0.85
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303016 p.Val29Ala missense_variant 0.22
fbiC 1303021 p.Arg31* stop_gained 0.22
Rv1258c 1406760 c.580_581insC frameshift_variant 0.93
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.87
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.85
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ribD 2986827 c.-12G>A upstream_gene_variant 0.83
Rv2752c 3065881 p.Gly104Asp missense_variant 0.16
thyA 3073806 c.666C>G synonymous_variant 0.14
ald 3086731 c.-89A>G upstream_gene_variant 0.93
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448567 p.His22Asp missense_variant 0.14
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiA 3640390 c.-153A>G upstream_gene_variant 0.5
rpoA 3878461 p.Asp16Gly missense_variant 0.17
embC 4239842 c.-21C>A upstream_gene_variant 0.24
embC 4242476 p.Pro872Ala missense_variant 0.25
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243346 c.114A>G synonymous_variant 0.86
embA 4243460 c.228C>T synonymous_variant 0.92
aftB 4267647 p.Asp397Gly missense_variant 1.0
ubiA 4269529 p.Ala102Gly missense_variant 0.38
whiB6 4338371 p.Thr51Pro missense_variant 0.92
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.96
gid 4407927 p.Glu92Asp missense_variant 0.89