TB-Profiler result

Run: SRR023449
Summary

Run ID: SRR023449

Sample name:

Date: 02-04-2023 14:12:09

Number of reads: 6138149

Percentage reads mapped: 93.59

Strain: lineage2.2.1

Drug-resistance: RR-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 0.99
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.98
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 761139 p.His445Tyr missense_variant 1.0 rifampicin
pncA 2288713 p.Thr177Pro missense_variant 0.23 pyrazinamide
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 0.99
gyrA 9304 p.Gly668Asp missense_variant 0.99
fgd1 491014 p.Thr78Pro missense_variant 0.36
fgd1 491324 p.Val181Gly missense_variant 0.43
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 0.98
mshA 576594 p.Val416Gly missense_variant 0.23
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 759827 p.Ser7Arg missense_variant 0.2
rpoB 759831 p.Thr9Pro missense_variant 0.28
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 766632 p.Val1088Gly missense_variant 0.29
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.99
mmpL5 776182 p.Asp767Asn missense_variant 0.99
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 0.99
rplC 801287 p.Val160Gly missense_variant 0.21
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
Rv1258c 1407084 p.Val86Gly missense_variant 0.22
rrs 1471659 n.-187C>T upstream_gene_variant 0.99
rpsA 1834177 c.636A>C synonymous_variant 0.99
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918060 p.Lys41Gln missense_variant 0.15
tlyA 1918181 p.Val81Gly missense_variant 0.33
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155778 p.Thr112Pro missense_variant 0.39
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168470 p.Thr715Pro missense_variant 0.26
PPE35 2169320 p.Leu431Phe missense_variant 0.18
PPE35 2169974 c.639T>G synonymous_variant 0.34
Rv1979c 2221889 p.Val426Ile missense_variant 0.98
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518300 c.186T>G synonymous_variant 0.31
ahpC 2726338 p.Val49Gly missense_variant 0.4
ahpC 2726341 p.Val50Gly missense_variant 0.31
folC 2746314 p.Arg429Trp missense_variant 0.14
pepQ 2859904 p.Val172Gly missense_variant 0.38
pepQ 2860253 p.Thr56Pro missense_variant 0.3
ald 3086788 c.-32T>C upstream_gene_variant 0.99
fbiD 3339273 c.156T>G synonymous_variant 0.25
fbiD 3339304 p.Thr63Pro missense_variant 0.33
fbiD 3339626 p.His170Pro missense_variant 0.38
fbiD 3339652 p.Thr179Ser missense_variant 0.2
fbiD 3339660 c.543C>A synonymous_variant 0.2
fbiD 3339688 p.Thr191Pro missense_variant 0.29
Rv3083 3449318 p.Glu272Gly missense_variant 0.23
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.97
Rv3236c 3612422 p.Val232Gly missense_variant 0.28
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
rpoA 3878059 p.Val150Gly missense_variant 0.24
ddn 3986994 p.Thr51Pro missense_variant 0.21
clpC1 4039566 p.Val380Gly missense_variant 0.36
embC 4240646 p.Phe262Val missense_variant 0.39
embC 4242326 p.Thr822Pro missense_variant 0.25
embC 4242341 p.Thr827Pro missense_variant 0.35
embA 4242643 c.-590C>T upstream_gene_variant 0.98
embC 4242822 p.Val987Gly missense_variant 0.28
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244217 p.Thr329Pro missense_variant 0.26
embA 4244605 p.Val458Gly missense_variant 0.38
embA 4244668 p.Val479Gly missense_variant 0.29
embA 4244905 p.Val558Gly missense_variant 0.45
embA 4246085 p.Glu951Asp missense_variant 0.99
embB 4247822 p.Thr437Pro missense_variant 0.47
embB 4248663 p.Val717Gly missense_variant 0.28
aftB 4267647 p.Asp397Gly missense_variant 1.0
ethA 4326925 p.Ser183Arg missense_variant 0.41
whiB6 4338536 c.-15G>T upstream_gene_variant 0.99
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