TB-Profiler result

Run: SRR17040823

Summary

Run ID: SRR17040823

Sample name:

Date: 03-04-2023 17:48:26

Number of reads: 664945

Percentage reads mapped: 99.47

Strain: 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 1.0
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 1.0
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 1.0
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 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289057 p.Pro62Leu missense_variant 1.0 pyrazinamide
pncA 2289121 p.Tyr41His missense_variant 0.11 pyrazinamide
eis 2715346 c.-14C>T upstream_gene_variant 1.0 kanamycin, amikacin
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
ethA 4327363 c.110delA frameshift_variant 1.0 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 491238 c.456C>A synonymous_variant 0.15
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575751 p.Gly135Val missense_variant 0.12
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 762471 p.Ile889Phe missense_variant 0.22
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764831 p.Glu488Gln missense_variant 1.0
rpoC 765043 c.1674G>A synonymous_variant 1.0
rpoC 765437 p.Lys690* stop_gained 0.29
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1305457 p.Pro843Thr missense_variant 0.18
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
Rv1258c 1407019 p.Val108Ile missense_variant 0.14
embR 1417158 p.Pro64Ser missense_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474241 n.584G>C non_coding_transcript_exon_variant 0.14
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918152 c.213C>T synonymous_variant 0.13
katG 2154653 p.Asp487Asn missense_variant 0.11
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2156095 p.Pro6Gln missense_variant 0.11
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169127 p.Val496Ile missense_variant 0.12
PPE35 2169593 c.1020C>T synonymous_variant 0.12
PPE35 2169725 c.888T>C synonymous_variant 0.11
PPE35 2169943 p.Leu224Ile missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518415 p.Pro101Thr missense_variant 0.13
eis 2714868 c.465C>T synonymous_variant 0.12
eis 2714884 p.His150Arg missense_variant 0.12
eis 2715048 c.285C>G synonymous_variant 0.15
folC 2746725 p.Pro292Thr missense_variant 0.13
pepQ 2859550 p.Phe290Ser missense_variant 0.1
thyX 3068000 c.-55G>T upstream_gene_variant 0.14
ald 3086731 c.-89A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449239 p.Arg246Cys missense_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612139 c.978T>C synonymous_variant 0.12
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiA 3640567 p.Gly9Arg missense_variant 0.13
fbiB 3640668 c.-867C>T upstream_gene_variant 0.12
fbiB 3641532 c.-3A>G upstream_gene_variant 0.12
fbiB 3642140 c.606C>T synonymous_variant 0.31
fbiB 3642492 p.Asp320Tyr missense_variant 0.14
rpoA 3877873 p.Gly212Val missense_variant 0.14
rpoA 3878630 c.-123G>C upstream_gene_variant 0.36
clpC1 4039619 c.1086G>T synonymous_variant 0.14
clpC1 4040195 c.510G>A synonymous_variant 0.15
panD 4044341 c.-60C>A upstream_gene_variant 0.17
embC 4240572 p.Gly237Val missense_variant 0.14
embC 4241462 p.Arg534Ser missense_variant 0.13
embA 4242391 c.-842G>T upstream_gene_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243346 c.114A>G synonymous_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244447 c.1215G>T synonymous_variant 0.11
embB 4245833 c.-681G>A upstream_gene_variant 0.15
embB 4247406 p.Ser298Leu missense_variant 0.11
aftB 4267435 p.Pro468Thr missense_variant 0.12
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4269566 c.-730C>A upstream_gene_variant 0.13
aftB 4269621 c.-785C>G upstream_gene_variant 0.12
whiB6 4338371 p.Thr51Pro missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407612 c.591T>C synonymous_variant 0.1
gid 4407927 p.Glu92Asp missense_variant 1.0