TB-Profiler result

Run: SRR1175047
Summary

Run ID: SRR1175047

Sample name:

Date: 03-04-2023 03:36:40

Number of reads: 267422

Percentage reads mapped: 96.84

Strain: lineage4

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
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
katG 2155597 p.Ala172Val missense_variant 1.0 isoniazid
ahpC 2726141 c.-52C>T upstream_gene_variant 1.0 isoniazid
embB 4247730 p.Gly406Ala missense_variant 1.0 ethambutol
embB 4249583 p.Asp1024Asn missense_variant 1.0 ethambutol
ethA 4327484 c.-11A>G upstream_gene_variant 1.0 ethionamide
pncA 2288565 c.377_*115del frameshift_variant&stop_lost&splice_region_variant 1.0 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 7383 p.Tyr28His missense_variant 0.2
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8040 p.Gly247Ser missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 765941 p.Lys858* stop_gained 0.29
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471666 n.-180A>G upstream_gene_variant 0.14
rrl 1474944 n.1287G>T non_coding_transcript_exon_variant 0.17
rrl 1476056 n.2399G>A non_coding_transcript_exon_variant 1.0
rrl 1476157 n.2500T>A non_coding_transcript_exon_variant 0.25
PPE35 2168584 p.Gly677Ser missense_variant 0.15
PPE35 2168666 c.1947T>C synonymous_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 2714845 p.Val163Ala missense_variant 0.29
ahpC 2726734 p.Gly181Ala missense_variant 1.0
Rv2752c 3065824 p.Pro123Leu missense_variant 1.0
thyX 3067587 p.Pro120Leu missense_variant 0.33
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087850 p.Ser344Trp missense_variant 0.33
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
rpoA 3878417 p.Gly31Ser missense_variant 1.0
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
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