TB-Profiler result

Run: SRR4037818
Summary

Run ID: SRR4037818

Sample name:

Date: 04-04-2023 07:41:39

Number of reads: 1752824

Percentage reads mapped: 99.43

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 761106 p.Met434Val missense_variant 0.2 rifampicin
katG 2154179 c.1932delC frameshift_variant 0.13 isoniazid
embC 4240725 p.Gly288Val missense_variant 0.12 ethambutol
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 575570 c.225_226dupTG frameshift_variant 0.17
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 575966 p.Val207Ile missense_variant 0.14
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 760734 p.Val310Phe missense_variant 0.12
rpoB 761122 p.Pro439Gln missense_variant 0.15
rpoB 761418 p.Ala538Ser missense_variant 0.17
rpoB 761611 p.Gly602Val missense_variant 0.18
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 767265 p.Ala1299Glu missense_variant 0.18
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776075 c.2406C>A synonymous_variant 0.14
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 777268 p.Leu405Met missense_variant 0.25
mmpL5 777371 c.1110C>A synonymous_variant 0.14
mmpL5 777575 p.Met302Ile missense_variant 0.17
mmpL5 777592 p.Ser297Pro missense_variant 0.17
mmpL5 777613 p.Gly290Trp missense_variant 0.15
mmpL5 778086 c.394delG frameshift_variant 0.12
mmpL5 778183 p.Pro100Thr missense_variant 0.12
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302951 c.21G>T synonymous_variant 0.18
fbiC 1303062 c.132G>T synonymous_variant 0.17
fbiC 1303148 p.Ala73Val missense_variant 0.14
fbiC 1304643 p.Lys571Asn missense_variant 0.14
fbiC 1304696 p.Trp589Leu missense_variant 0.12
fbiC 1305402 p.His824Gln missense_variant 0.12
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1673592 c.-610G>T upstream_gene_variant 0.15
inhA 1674057 c.-145C>A upstream_gene_variant 0.13
fabG1 1674152 p.Pro238Gln missense_variant 0.14
inhA 1674434 p.Val78Ala missense_variant 0.11
inhA 1674859 p.Glu220* stop_gained 0.13
rpsA 1833761 p.Val74Phe missense_variant 0.12
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918006 p.Ala23Thr missense_variant 0.18
ndh 2103173 c.-132delG upstream_gene_variant 0.18
katG 2154213 c.1899C>A synonymous_variant 0.13
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155744 p.Gly123Val missense_variant 0.12
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169320 p.Leu431Phe missense_variant 0.37
PPE35 2170087 p.Ala176Ser missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 0.96
pncA 2290017 c.-776C>A upstream_gene_variant 0.12
eis 2714307 c.1025delC frameshift_variant 0.14
eis 2715177 c.156C>A synonymous_variant 0.2
folC 2747685 c.-87C>A upstream_gene_variant 0.14
pepQ 2859700 p.Gly240Val missense_variant 0.12
pepQ 2860074 p.Glu115Asp missense_variant 0.25
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087326 c.507C>A synonymous_variant 0.13
ald 3087382 p.Asn188Ser missense_variant 0.11
fprA 3473868 c.-139G>T upstream_gene_variant 0.14
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474227 p.Pro74His missense_variant 0.18
fprA 3474767 p.Gly254Asp missense_variant 0.18
fprA 3474996 c.990C>A synonymous_variant 0.33
fprA 3475022 p.Gly339Val missense_variant 0.25
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiA 3641518 c.978delT frameshift_variant 0.12
fbiB 3641955 p.Gly141Arg missense_variant 0.17
clpC1 4038386 p.Leu773Phe missense_variant 0.12
clpC1 4038401 p.Leu768Phe missense_variant 0.12
clpC1 4039276 p.Ala477Thr missense_variant 0.14
embC 4240640 c.778C>A synonymous_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243126 c.-107G>T upstream_gene_variant 0.17
embA 4243414 p.Pro61His missense_variant 0.13
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244370 p.Arg380Cys missense_variant 0.17
embA 4245404 c.2172C>A synonymous_variant 0.25
embA 4245466 p.Pro745His missense_variant 0.13
embA 4245579 p.Ser783Pro missense_variant 0.14
embA 4245997 p.Trp922Leu missense_variant 0.12
embB 4246403 c.-111G>T upstream_gene_variant 0.13
embB 4246892 p.Asp127Tyr missense_variant 0.13
embB 4247298 p.Pro262Gln missense_variant 0.13
embB 4247320 c.809delC frameshift_variant 0.12
embB 4247921 p.His470Asn missense_variant 0.13
embB 4248902 p.Thr797Ala missense_variant 0.14
aftB 4267547 c.1290C>A synonymous_variant 0.15
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268684 p.Gln51His missense_variant 0.13
ubiA 4269115 p.Arg240Leu missense_variant 0.15
ethR 4327587 p.Arg13Ser missense_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407620 p.Tyr195His missense_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0