TB-Profiler result

Run: SRR18714885
Summary

Run ID: SRR18714885

Sample name:

Date: 03-04-2023 20:09:13

Number of reads: 3747281

Percentage reads mapped: 99.72

Strain: lineage4.3.3

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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.3 Euro-American (LAM) LAM;T RD115 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
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289157 c.84_85insG frameshift_variant 0.97 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 0.99
gyrA 8040 p.Gly247Ser missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.12
mshA 576442 p.Cys365Trp missense_variant 0.2
mshA 576456 p.Val370Gly missense_variant 0.24
mshA 576616 c.1269G>C synonymous_variant 0.21
rpoB 759939 p.Pro45Thr missense_variant 1.0
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 766667 p.Ser1100Ala missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777883 p.Gly200Arg missense_variant 0.19
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673553 p.Asp38Glu missense_variant 0.34
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102052 p.Gly331Arg missense_variant 1.0
PPE35 2170065 p.Ala183Gly missense_variant 0.57
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 1.0
kasA 2519071 p.Asp319Glu missense_variant 0.22
pepQ 2860159 p.Ala87Gly missense_variant 0.19
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339490 p.Leu125Ile missense_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.8
fbiD 3339751 p.Ala212Pro missense_variant 0.2
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568425 c.255T>C synonymous_variant 0.25
rpoA 3878641 c.-134C>G upstream_gene_variant 0.73
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embC 4240409 p.Pro183Ala missense_variant 0.41
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244823 p.Val531Leu missense_variant 1.0
embB 4246527 p.Ala5Gly missense_variant 0.4
embB 4246584 p.Arg24Pro missense_variant 0.24
embB 4248316 c.1803C>T synonymous_variant 1.0
ethA 4326903 p.Val191Met missense_variant 1.0
whiB6 4338200 p.Asp108His missense_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408009 p.Val65Ala missense_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0