TB-Profiler result

Run: SRR1172889
Summary

Run ID: SRR1172889

Sample name:

Date: 03-04-2023 03:12:38

Number of reads: 444598

Percentage reads mapped: 96.19

Strain: lineage4.3

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
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 761110 p.Asp435Val missense_variant 1.0 rifampicin
fabG1 1673432 c.-8T>A upstream_gene_variant 1.0 isoniazid
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288847 p.Gly132Ala missense_variant 1.0 pyrazinamide
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
ethA 4327484 c.-11A>G 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 8040 p.Gly247Ser missense_variant 1.0
gyrA 9091 p.Ala597Asp missense_variant 0.2
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303383 c.453G>T synonymous_variant 0.33
fbiC 1303399 p.Gln157* stop_gained 0.33
fbiC 1304875 p.Ile649Val missense_variant 0.2
embR 1416835 c.513T>A synonymous_variant 0.29
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1476056 n.2399G>A non_coding_transcript_exon_variant 1.0
inhA 1673514 c.-688G>T upstream_gene_variant 0.12
tlyA 1917916 c.-24C>T upstream_gene_variant 0.22
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2167929 p.Ser895Leu missense_variant 0.2
Rv1979c 2223051 p.Glu38Asp missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 1.0
eis 2714461 p.Gln291Arg missense_variant 0.12
Rv2752c 3065314 p.Glu293Ala missense_variant 0.25
Rv2752c 3065824 p.Pro123Leu missense_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
alr 3840341 c.1080C>A synonymous_variant 0.22
alr 3841058 c.363G>T synonymous_variant 0.18
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embC 4240972 c.1110C>T synonymous_variant 0.25
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244303 p.Asn357Lys missense_variant 0.4
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0
gid 4407912 c.160_290del frameshift_variant 1.0