TB-Profiler result

Run: SRR1011521
Summary

Run ID: SRR1011521

Sample name:

Date: 02-04-2023 15:55:08

Number of reads: 11213988

Percentage reads mapped: 99.34

Strain: lineage4.5

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 1.0
lineage4.5 Euro-American H;T RD122 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
gyrA 7581 p.Asp94Tyr missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761109 p.Asp435Tyr missense_variant 1.0 rifampicin
rpoB 761137 p.Thr444Ile missense_variant 1.0 rifampicin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
pncA 2289016 p.Thr76Pro missense_variant 1.0 pyrazinamide
eis 2715342 c.-10G>C upstream_gene_variant 0.99 kanamycin, kanamycin
folC 2747471 p.Ile43Ser missense_variant 1.0 para-aminosalicylic_acid
embB 4248002 p.Gln497Lys missense_variant 1.0 ethambutol
gid 4407695 p.Glu170* stop_gained 1.0 streptomycin
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 7892 c.591G>A synonymous_variant 0.99
gyrA 9304 p.Gly668Asp missense_variant 1.0
ccsA 620029 c.139C>T synonymous_variant 0.93
rpoB 760305 p.Arg167Cys missense_variant 1.0
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 1475998 n.2341C>A non_coding_transcript_exon_variant 1.0
inhA 1674265 p.Ala22Ser missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154418 p.Val565Gly missense_variant 1.0
PPE35 2167797 c.2815dupC frameshift_variant 0.61
PPE35 2170137 p.Ser159Leu missense_variant 1.0
PPE35 2170568 p.Ile15Met missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv2752c 3065439 c.753C>T synonymous_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
rpoA 3878575 c.-68C>T upstream_gene_variant 1.0
rpoA 3878580 c.-73A>G upstream_gene_variant 1.0
clpC1 4038318 p.Pro796Leu missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338593 c.-73delT upstream_gene_variant 1.0
whiB6 4338596 c.-75G>C upstream_gene_variant 1.0