TB-Profiler result

Run: SRR1167341
Summary

Run ID: SRR1167341

Sample name:

Date: 03-04-2023 02:18:40

Number of reads: 4314051

Percentage reads mapped: 99.55

Strain: lineage4.3.3

Drug-resistance: Pre-XDR-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 0.98
lineage4.3 Euro-American (LAM) mainly-LAM None 0.92
lineage4.3.3 Euro-American (LAM) LAM;T RD115 0.93
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
gyrA 7570 p.Ala90Val missense_variant 0.95 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761110 p.Asp435Gly missense_variant 0.92 rifampicin
rpoB 761161 p.Leu452Pro missense_variant 0.91 rifampicin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.94 kanamycin, capreomycin, aminoglycosides, amikacin
fabG1 1673432 c.-8T>A upstream_gene_variant 0.94 isoniazid
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288785 c.456dupC frameshift_variant 0.95 pyrazinamide, pyrazinamide
embB 4247429 p.Met306Val missense_variant 0.88 ethambutol
ethA 4327484 c.-11A>G upstream_gene_variant 0.97 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 0.91
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 575907 p.Ala187Val missense_variant 0.15
rpoB 763123 p.Ile1106Thr missense_variant 0.9
rpoC 764995 c.1626C>G synonymous_variant 0.93
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
rrl 1476056 n.2399G>A non_coding_transcript_exon_variant 0.94
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169320 p.Leu431Phe missense_variant 0.2
Rv1979c 2223051 p.Glu38Asp missense_variant 0.92
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 0.96
Rv2752c 3065824 p.Pro123Leu missense_variant 0.92
thyA 3073868 p.Thr202Ala missense_variant 0.92
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.13
ubiA 4269271 p.Val188Ala missense_variant 0.94
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 0.9