TB-Profiler result

Run: SRR21277810
Summary

Run ID: SRR21277810

Sample name:

Date: 04-04-2023 01:45:07

Number of reads: 17797058

Percentage reads mapped: 98.3

Strain: lineage2.2.1.1

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
lineage2.2.1.1 East-Asian (Beijing) Beijing-RD150 RD105;RD207;RD181;RD150 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 761100 p.Gln432Lys 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
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576451 c.1104G>A synonymous_variant 0.12
mshA 576459 p.Ala371Asp missense_variant 0.12
ccsA 620128 p.Gly80Trp missense_variant 0.12
ccsA 620133 c.243G>T synonymous_variant 0.11
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 762306 p.Pro834Ser missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763943 p.Asp192Asn missense_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 777327 p.Ala385Val missense_variant 0.17
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304207 p.Arg426Leu missense_variant 0.17
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
Rv1258c 1407001 p.Ala114Ser missense_variant 0.13
Rv1258c 1407003 p.Ala113Val missense_variant 0.18
Rv1258c 1407539 c.-199C>A upstream_gene_variant 0.1
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 0.95
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155746 c.366C>T synonymous_variant 0.12
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518871 p.His253Tyr missense_variant 1.0
kasA 2519083 c.969C>T synonymous_variant 0.12
eis 2714846 p.Val163Ile missense_variant 1.0
folC 2746332 p.Glu423* stop_gained 0.1
pepQ 2860158 p.Ala87Val missense_variant 0.12
thyX 3067276 p.Pro224Thr missense_variant 0.14
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 1.0
fbiB 3642012 p.Gln160* stop_gained 0.11
alr 3841070 c.351C>T synonymous_variant 0.11
alr 3841139 c.282C>T synonymous_variant 0.18
embA 4242418 c.-815C>A upstream_gene_variant 0.2
embC 4242497 p.Arg879Trp missense_variant 0.33
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244279 c.1047G>T synonymous_variant 0.12
embA 4244570 c.1338C>T synonymous_variant 0.11
embB 4247869 c.1356G>A synonymous_variant 0.11
embB 4247878 c.1365G>A synonymous_variant 0.23
embB 4248115 c.1602C>T synonymous_variant 1.0
aftB 4267647 p.Asp397Gly missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0