TB-Profiler result

Run: SRR1146370
Summary

Run ID: SRR1146370

Sample name:

Date: 02-04-2023 21:34:25

Number of reads: 5303743

Percentage reads mapped: 98.91

Strain: lineage3;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
lineage3 East-African-Indian CAS RD750 0.2
lineage2 East-Asian Beijing RD105 0.82
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.74
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.8
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 0.9 rifampicin
rpsL 781822 p.Lys88Arg missense_variant 0.75 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.9 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 0.76 isoniazid
pncA 2289248 c.-7T>C upstream_gene_variant 0.86 pyrazinamide
embA 4243221 c.-12C>T upstream_gene_variant 0.77 ethambutol
embB 4247513 p.Tyr334His missense_variant 0.69 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 575907 p.Ala187Val missense_variant 0.62
ccsA 620625 p.Ile245Met missense_variant 0.78
rpoB 760836 p.Glu344Gln missense_variant 0.3
rpoC 762434 c.-936T>G upstream_gene_variant 0.21
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764817 p.Val483Gly missense_variant 0.74
rpoC 766645 p.Glu1092Asp missense_variant 0.78
rpoC 767236 c.3867G>A synonymous_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 0.77
mmpS5 779615 c.-710C>G upstream_gene_variant 0.74
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.75
embR 1416890 p.Leu153Arg missense_variant 0.26
rrs 1471659 n.-187C>T upstream_gene_variant 0.99
inhA 1674480 c.279T>C synonymous_variant 0.12
rpsA 1834177 c.636A>C synonymous_variant 0.81
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2154811 p.Gln434Pro missense_variant 0.16
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 0.16
ahpC 2726105 c.-88G>A upstream_gene_variant 0.23
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087532 p.Ala238Asp missense_variant 0.72
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612229 c.888C>T synonymous_variant 0.77
Rv3236c 3612813 p.Thr102Ala missense_variant 0.78
fbiB 3642098 c.564G>A synonymous_variant 0.12
alr 3840916 p.Pro169Ser missense_variant 0.21
panD 4044170 c.112C>T synonymous_variant 0.14
embC 4241664 p.Gly601Val missense_variant 0.17
embC 4242075 p.Arg738Gln missense_variant 0.16
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.69
embB 4247518 c.1005C>T synonymous_variant 0.31
aftB 4267647 p.Asp397Gly missense_variant 0.74
aftB 4269339 c.-503C>T upstream_gene_variant 0.73
ethA 4327701 c.-228G>A upstream_gene_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 0.82
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 0.81