TB-Profiler result

Run: ERR137271
Summary

Run ID: ERR137271

Sample name:

Date: 31-03-2023 14:02:50

Number of reads: 8498307

Percentage reads mapped: 99.58

Strain: lineage4.2.1;lineage2.2.1

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
lineage2 East-Asian Beijing RD105 0.86
lineage4 Euro-American LAM;T;S;X;H None 0.15
lineage4.2 Euro-American H;T;LAM None 0.15
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.86
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.87
lineage4.2.1 Euro-American (TUR) H3;H4 None 0.15
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
rpoC 764822 p.Asp485Asn missense_variant 0.13 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.82 streptomycin
rpsL 781822 p.Lys88Arg missense_variant 0.14 streptomycin
inhA 1674048 c.-154G>A upstream_gene_variant 0.15 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288930 p.Ser104Arg missense_variant 0.16 pyrazinamide
pncA 2289231 p.Leu4Trp missense_variant 0.84 pyrazinamide
eis 2715342 c.-10G>A upstream_gene_variant 0.79 kanamycin
embA 4243221 c.-12C>T upstream_gene_variant 0.84 ethambutol
embB 4247399 p.Asn296His missense_variant 0.85 ethambutol
embB 4248003 p.Gln497Arg missense_variant 0.13 ethambutol
ethA 4327363 c.110delA frameshift_variant 0.82 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 491247 c.465C>T synonymous_variant 0.11
fgd1 491742 c.960T>C synonymous_variant 0.85
mshA 575907 p.Ala187Val missense_variant 0.81
ccsA 619969 p.Val27Ile missense_variant 0.12
ccsA 620625 p.Ile245Met missense_variant 0.83
rpoC 763031 c.-339T>C upstream_gene_variant 0.86
mmpL5 775639 p.Ile948Val missense_variant 0.99
mmpL5 776100 p.Thr794Ile missense_variant 0.87
mmpL5 776182 p.Asp767Asn missense_variant 0.87
mmpS5 779615 c.-710C>G upstream_gene_variant 0.9
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800665 c.-144A>G upstream_gene_variant 0.16
fbiC 1304253 c.1323G>T synonymous_variant 0.12
Rv1258c 1406760 c.580_581insC frameshift_variant 0.85
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.85
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.87
PPE35 2167926 p.Leu896Ser missense_variant 0.89
PPE35 2169866 c.747G>C synonymous_variant 0.2
PPE35 2169879 p.Phe245Cys missense_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ribD 2986827 c.-12G>A upstream_gene_variant 0.16
thyA 3073806 c.666C>G synonymous_variant 0.23
ald 3086731 c.-89A>G upstream_gene_variant 0.83
ald 3086742 c.-78A>C upstream_gene_variant 0.13
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 0.85
rpoA 3878416 p.Gly31Ala missense_variant 0.78
embC 4242425 p.Arg855Gly missense_variant 0.29
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243346 c.114A>G synonymous_variant 0.83
embA 4243460 c.228C>T synonymous_variant 0.84
embB 4249594 c.3081G>A synonymous_variant 0.12
aftB 4267647 p.Asp397Gly missense_variant 0.86
ethA 4326314 p.Thr387Ile missense_variant 0.17
ethA 4328376 c.-903G>C upstream_gene_variant 0.13
whiB6 4338371 p.Thr51Pro missense_variant 0.85
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.82
gid 4407927 p.Glu92Asp missense_variant 0.86