TB-Profiler result

Run: SRR1166818
Summary

Run ID: SRR1166818

Sample name:

Date: 03-04-2023 01:26:53

Number of reads: 1276141

Percentage reads mapped: 98.79

Strain: lineage4.8

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
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 0.99
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
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 1.0 kanamycin, capreomycin, aminoglycosides, amikacin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288805 p.Ala146Val missense_variant 1.0 pyrazinamide
embB 4247729 p.Gly406Ser missense_variant 1.0 ethambutol
embB 4249583 p.Asp1024Asn missense_variant 1.0 ethambutol
gid 4407830 p.Gln125* stop_gained 0.97 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
rpoC 764817 p.Val483Ala missense_variant 1.0
rpoC 765008 p.Leu547Val missense_variant 1.0
rpoC 766085 p.Pro906Ala missense_variant 1.0
rpoC 766611 p.Ser1081Tyr missense_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
atpE 1460992 c.-53A>C upstream_gene_variant 0.98
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
fabG1 1674110 p.Leu224Pro missense_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169320 p.Leu431Phe missense_variant 0.25
PPE35 2170100 c.513G>T synonymous_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518791 p.Ala226Val missense_variant 0.11
thyA 3074616 c.-145T>C upstream_gene_variant 0.12
thyA 3074637 c.-166A>G upstream_gene_variant 0.15
thyA 3074641 c.-170C>A upstream_gene_variant 0.17
fprA 3474987 c.981G>T synonymous_variant 0.12
alr 3840764 c.657G>C synonymous_variant 1.0
embC 4241045 p.Gly395Cys missense_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4248053 p.Pro514Ser missense_variant 0.12
aftB 4267407 p.Lys477Arg missense_variant 0.1
ethA 4326918 p.Thr186Pro missense_variant 1.0
ethR 4327036 c.-513G>T upstream_gene_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448497 c.-6_*1408del transcript_ablation 1.0