TB-Profiler result

Run: ERR4796896

Summary

Run ID: ERR4796896

Sample name:

Date: 16-08-2022 00:27:45

Number of reads: 2554578

Percentage reads mapped: 99.61

Strain: lineage4.8

Drug-resistance: 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
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 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 7582 p.Asp94Ala missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
rplC 801268 p.Cys154Arg missense_variant 1.0 linezolid
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 1.0 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289252 c.-11A>G upstream_gene_variant 1.0 pyrazinamide
ald 3087252 c.436_437dupGC frameshift_variant 1.0 cycloserine
embB 4248003 p.Gln497Arg missense_variant 1.0 ethambutol
ethA 4326889 c.584dupC frameshift_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
mshA 576108 p.Ala254Gly missense_variant 0.18
rpoB 761461 p.Arg552His missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpR5 779243 p.Val85Gly missense_variant 0.63
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1475952 n.2295A>C non_coding_transcript_exon_variant 0.19
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168149 p.Pro822Ser missense_variant 1.0
PPE35 2170065 p.Ala183Gly missense_variant 0.25
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pepQ 2860159 p.Ala87Gly missense_variant 0.15
rpoA 3878658 c.-151A>C upstream_gene_variant 0.2
clpC1 4039729 p.Asp326Asn missense_variant 1.0
embC 4240409 p.Pro183Ala missense_variant 0.35
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 0.99
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0