TB-Profiler result

Run: SRR6485094
Summary

Run ID: SRR6485094

Sample name:

Date: 04-04-2023 15:07:01

Number of reads: 1618652

Percentage reads mapped: 99.64

Strain: lineage2.2.1

Drug-resistance: MDR-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
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 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288924 c.317delT frameshift_variant 1.0 pyrazinamide, pyrazinamide
eis 2715342 c.-10G>A upstream_gene_variant 1.0 kanamycin
embB 4247574 p.Asp354Ala missense_variant 1.0 ethambutol
ethA 4327480 c.-7T>C upstream_gene_variant 1.0 ethionamide
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 0.92
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.16
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 765617 p.Glu750Gln 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
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471801 n.-45A>T upstream_gene_variant 0.67
fabG1 1673346 c.-94C>G upstream_gene_variant 0.17
fabG1 1673349 c.-91G>C upstream_gene_variant 0.18
fabG1 1673380 c.-60C>G upstream_gene_variant 0.38
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
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.25
PPE35 2170053 p.Thr187Ser missense_variant 0.25
PPE35 2170157 p.Ala152Ser missense_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714424 c.909C>A synonymous_variant 0.33
Rv2752c 3064981 p.Arg404Leu missense_variant 0.16
Rv2752c 3065400 c.792A>G synonymous_variant 0.13
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
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4243050 c.3189delG frameshift_variant 0.2
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4245463 p.Asp744Ala missense_variant 0.22
embB 4246548 p.Pro12Gln missense_variant 0.23
embB 4246555 c.42G>C synonymous_variant 0.27
embB 4246556 p.Ala15Pro missense_variant 0.27
aftB 4267647 p.Asp397Gly missense_variant 1.0
ethR 4326961 c.-588G>C upstream_gene_variant 0.13
ethR 4326964 c.-585G>A upstream_gene_variant 0.13
ethR 4326970 c.-579G>T upstream_gene_variant 0.12
ethA 4328266 c.-793A>T upstream_gene_variant 0.13
whiB6 4338563 c.-42G>T upstream_gene_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