TB-Profiler result

Run: SRR6789637
Summary

Run ID: SRR6789637

Sample name:

Date: 04-04-2023 16:04:32

Number of reads: 1129145

Percentage reads mapped: 97.6

Strain: 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 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 761140 p.His445Leu missense_variant 1.0 rifampicin
fabG1 1673432 c.-8T>A upstream_gene_variant 1.0 isoniazid
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
gyrB 7195 p.Met652Ile missense_variant 0.12
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
ccsA 619978 c.89delT frameshift_variant 0.12
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 761152 p.Leu449Gln missense_variant 0.13
rpoB 761659 p.Pro618Gln missense_variant 0.13
rpoB 761699 p.Asp631Glu missense_variant 0.25
rpoB 761739 p.Glu645* stop_gained 0.17
rpoB 761742 p.Glu646* stop_gained 0.17
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 0.96
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303983 c.1053C>T synonymous_variant 0.13
fbiC 1304208 c.1278C>T synonymous_variant 0.17
fbiC 1304271 c.1341C>A synonymous_variant 0.17
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673380 c.-60C>G upstream_gene_variant 0.31
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834971 p.Leu477Pro missense_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.23
PPE35 2170053 p.Thr187Ser missense_variant 0.19
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
thyX 3067421 c.525G>A synonymous_variant 0.13
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568693 c.-14A>G upstream_gene_variant 0.12
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3642879 c.1345T>C stop_lost&splice_region_variant 0.12
alr 3841266 p.Leu52Pro missense_variant 0.1
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243190 c.-43G>C upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244813 c.1581C>T synonymous_variant 0.11
embA 4246000 p.Arg923His missense_variant 0.11
embB 4246544 p.Thr11Pro missense_variant 0.26
embB 4246548 p.Pro12Gln missense_variant 0.29
embB 4246555 c.42G>C synonymous_variant 0.31
embB 4246556 p.Ala15Pro missense_variant 0.31
aftB 4267340 c.1497G>T synonymous_variant 0.12
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268585 c.252G>A synonymous_variant 0.15
ethR 4328158 p.Val204Met 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