TB-Profiler result

Run: SRR10379879
Summary

Run ID: SRR10379879

Sample name:

Date: 02-04-2023 17:19:10

Number of reads: 2747161

Percentage reads mapped: 99.54

Strain: lineage4.2.1;lineage2.2.1

Drug-resistance: HR-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 0.84
lineage4 Euro-American LAM;T;S;X;H None 0.15
lineage4.2 Euro-American H;T;LAM None 0.14
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.86
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.85
lineage4.2.1 Euro-American (TUR) H3;H4 None 0.11
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
rpsL 781822 p.Lys88Arg missense_variant 0.14 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.12 isoniazid
pncA 2288694 c.547dupG frameshift_variant 0.11 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 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491247 c.465C>T synonymous_variant 0.14
fgd1 491742 c.960T>C synonymous_variant 0.84
mshA 575907 p.Ala187Val missense_variant 0.85
mshA 576108 p.Ala254Gly missense_variant 0.21
ccsA 619969 p.Val27Ile missense_variant 0.11
ccsA 620625 p.Ile245Met missense_variant 0.87
rpoC 763031 c.-339T>C upstream_gene_variant 0.89
rpoC 764817 p.Val483Gly missense_variant 0.15
rpoC 766645 p.Glu1092Asp missense_variant 0.92
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.92
mmpL5 776182 p.Asp767Asn missense_variant 0.84
mmpL5 776517 p.Met655Thr missense_variant 0.82
mmpS5 779615 c.-710C>G upstream_gene_variant 0.93
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.84
rrs 1471659 n.-187C>T upstream_gene_variant 0.99
rpsA 1834177 c.636A>C synonymous_variant 0.8
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918196 p.Cys86Tyr missense_variant 0.15
katG 2154724 p.Arg463Leu missense_variant 0.9
PPE35 2167926 p.Leu896Ser missense_variant 0.8
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ald 3086742 c.-78A>C upstream_gene_variant 0.11
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474656 p.Asp217Ala missense_variant 0.88
Rv3236c 3612813 p.Thr102Ala missense_variant 0.88
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.85
embB 4249594 c.3081G>A synonymous_variant 0.15
aftB 4267647 p.Asp397Gly missense_variant 0.84
ubiA 4269721 p.Ala38Val missense_variant 0.13
ethA 4326632 p.His281Pro missense_variant 0.16
ethA 4328376 c.-903G>C upstream_gene_variant 0.18
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.9
gid 4407927 p.Glu92Asp missense_variant 0.86