TB-Profiler result

Run: SRR3082113
Summary

Run ID: SRR3082113

Sample name:

Date: 04-04-2023 04:54:01

Number of reads: 1038519

Percentage reads mapped: 99.57

Strain: lineage2.2

Drug-resistance: Pre-XDR-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
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
gyrA 7582 p.Asp94Gly missense_variant 0.94 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781822 p.Lys88Arg missense_variant 1.0 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288920 p.Gly108Arg missense_variant 1.0 pyrazinamide
embA 4243221 c.-12C>T upstream_gene_variant 1.0 ethambutol
embB 4247513 p.Tyr334His missense_variant 1.0 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 7290 c.-12A>G upstream_gene_variant 0.2
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 620625 p.Ile245Met missense_variant 1.0
rpoB 761240 c.1434C>T synonymous_variant 0.11
rpoB 761710 p.Val635Asp missense_variant 0.17
rpoB 761713 p.Val636Asp missense_variant 0.18
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764817 p.Val483Gly missense_variant 1.0
rpoC 766645 p.Glu1092Asp missense_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 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
Rv1258c 1406804 c.537G>T synonymous_variant 0.33
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471757 n.-89T>A upstream_gene_variant 0.25
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155352 p.Arg254Cys missense_variant 0.17
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169309 p.Gly435Asp missense_variant 0.22
Rv1979c 2222097 c.1068G>A synonymous_variant 0.17
Rv1979c 2222377 p.Val263Ala missense_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518526 c.416delC frameshift_variant 0.12
pepQ 2859929 p.Arg164Trp missense_variant 0.17
ribD 2986767 c.-71delC upstream_gene_variant 0.15
Rv2752c 3066369 c.-178C>T upstream_gene_variant 0.17
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087532 p.Ala238Asp missense_variant 0.96
ald 3087926 c.1107G>A synonymous_variant 0.22
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612229 c.888C>T synonymous_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiA 3641150 p.Leu203Pro missense_variant 0.22
rpoA 3878203 p.Pro102Leu missense_variant 0.11
embC 4241487 p.Leu542Pro missense_variant 0.11
embC 4242491 c.2632_2638delGACAGGG frameshift_variant 0.25
embC 4242502 c.2642_2643insCTGTCCC frameshift_variant 0.25
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243264 p.Arg11Gln missense_variant 0.12
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4248585 p.Arg691His missense_variant 0.12
aftB 4267053 p.Tyr595Cys missense_variant 0.11
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