TB-Profiler result

Run: SRR23310984
Summary

Run ID: SRR23310984

Sample name:

Date: 14-03-2023 05:43:11

Number of reads: 3720745

Percentage reads mapped: 99.56

Strain: lineage4.2.1;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 0.25
lineage4.2 Euro-American H;T;LAM None 0.78
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.27
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.23
lineage4.2.1 Euro-American (TUR) H3;H4 None 0.76
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
rpsL 781687 p.Lys43Arg missense_variant 0.27 streptomycin
rpsL 781822 p.Lys88Arg missense_variant 0.72 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.76 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288928 p.Gly105Val missense_variant 0.2 pyrazinamide
eis 2715344 c.-12C>T upstream_gene_variant 0.75 kanamycin
embB 4247399 p.Asn296His missense_variant 0.26 ethambutol
embB 4247402 p.Ser297Ala missense_variant 0.73 ethambutol
ethA 4327363 c.107delA frameshift_variant 0.25 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
gyrA 9647 c.2346C>G synonymous_variant 0.17
fgd1 491247 c.465C>T synonymous_variant 0.73
fgd1 491742 c.960T>C synonymous_variant 0.24
mshA 575907 p.Ala187Val missense_variant 0.26
mshA 576108 p.Ala254Gly missense_variant 0.17
mshA 576613 c.1266A>C synonymous_variant 0.18
mshA 576616 c.1269G>C synonymous_variant 0.21
ccsA 619969 p.Val27Ile missense_variant 0.81
ccsA 620625 p.Ile245Met missense_variant 0.21
rpoC 763031 c.-339T>C upstream_gene_variant 0.23
rpoC 764817 p.Val483Gly missense_variant 0.75
rpoC 764840 p.Ile491Val missense_variant 0.26
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775695 p.Ile929Thr missense_variant 0.26
mmpL5 776100 p.Thr794Ile missense_variant 0.24
mmpL5 776182 p.Asp767Asn missense_variant 0.21
mmpS5 779615 c.-710C>G upstream_gene_variant 0.3
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.23
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673553 p.Asp38Glu missense_variant 0.21
rpsA 1834177 c.636A>C synonymous_variant 0.29
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.2
PPE35 2167926 p.Leu896Ser missense_variant 0.19
PPE35 2169879 p.Phe245Cys missense_variant 0.73
PPE35 2170065 p.Ala183Gly missense_variant 0.22
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pepQ 2860159 p.Ala87Gly missense_variant 0.28
ald 3086731 c.-89A>G upstream_gene_variant 0.25
ald 3086742 c.-78A>C upstream_gene_variant 0.73
ald 3086788 c.-32T>C upstream_gene_variant 0.99
fbiD 3339734 p.Ala206Gly missense_variant 0.56
fprA 3473996 c.-10_-9insA upstream_gene_variant 1.0
whiB7 3568428 c.252A>C synonymous_variant 0.24
Rv3236c 3612813 p.Thr102Ala missense_variant 0.27
rpoA 3878641 c.-134C>G upstream_gene_variant 0.53
embC 4240409 p.Pro183Ala missense_variant 0.28
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243346 c.114A>G synonymous_variant 0.22
embA 4243460 c.228C>T synonymous_variant 0.29
embB 4246527 p.Ala5Gly missense_variant 0.43
embB 4246529 p.Ser6Arg missense_variant 0.29
embB 4248328 c.1815G>C synonymous_variant 0.18
embB 4249594 c.3081G>A synonymous_variant 0.82
aftB 4267647 p.Asp397Gly missense_variant 0.27
ethA 4326632 p.His281Pro missense_variant 0.74
ethA 4328376 c.-903G>C upstream_gene_variant 0.78
whiB6 4338371 p.Thr51Pro missense_variant 0.24
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.27
gid 4407927 p.Glu92Asp missense_variant 0.25