TB-Profiler result

Run: SRR4033158
Summary

Run ID: SRR4033158

Sample name:

Date: 04-04-2023 05:52:04

Number of reads: 1870701

Percentage reads mapped: 99.52

Strain: lineage2.2.1

Drug-resistance: RR-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 0.99
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 761139 p.His445Tyr missense_variant 1.0 rifampicin
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 490652 c.-131G>C upstream_gene_variant 0.11
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 0.96
mshA 576356 p.Ala337Thr missense_variant 0.12
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 761405 c.1599C>T synonymous_variant 0.18
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 765013 c.1644C>T synonymous_variant 0.97
rpoC 765281 p.Thr638Ala missense_variant 0.11
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
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1674455 p.Gly85Val missense_variant 0.15
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834225 c.684C>A synonymous_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2153970 p.Asp714Glu missense_variant 0.39
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169320 p.Leu431Phe missense_variant 0.28
PPE35 2169866 c.747G>C synonymous_variant 0.18
PPE35 2170239 c.373dupC frameshift_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2725954 c.-239C>T upstream_gene_variant 0.13
folC 2747693 c.-96delC upstream_gene_variant 0.11
Rv2752c 3064832 p.Ala454Thr missense_variant 0.13
thyX 3067195 c.751T>C stop_lost&splice_region_variant 0.11
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3642149 c.618delA frameshift_variant 0.14
fbiB 3642236 c.702G>A synonymous_variant 0.17
rpoA 3878604 c.-97G>T upstream_gene_variant 0.29
rpoA 3878641 c.-134C>G upstream_gene_variant 0.14
embC 4242425 p.Arg855Gly missense_variant 0.2
embC 4242513 c.2653delG frameshift_variant 0.29
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242818 c.-415C>T upstream_gene_variant 0.12
embC 4242822 p.Val987Gly missense_variant 0.2
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4243531 p.Thr100Ile missense_variant 0.13
embB 4246544 p.Thr11Pro missense_variant 0.11
embB 4246555 c.42G>C synonymous_variant 0.12
embB 4246556 p.Ala15Pro missense_variant 0.12
embB 4246563 p.Leu17Trp missense_variant 0.11
embB 4246567 c.54G>T synonymous_variant 0.17
embB 4247288 p.Ala259Thr missense_variant 0.15
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 4407674 c.528delT frameshift_variant 0.11
gid 4407927 p.Glu92Asp missense_variant 1.0