TB-Profiler result

Run: ERR2510724
Summary

Run ID: ERR2510724

Sample name:

Date: 31-03-2023 18:54:41

Number of reads: 2365224

Percentage reads mapped: 99.74

Strain: lineage4.8

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
lineage4.8 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.Asp94Gly missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761110 p.Asp435Val missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.96 streptomycin
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 2289202 p.Cys14Gly missense_variant 1.0 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
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
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304849 p.Asn640Ser missense_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
fabG1 1673380 c.-60C>G upstream_gene_variant 0.33
tlyA 1917846 c.-94C>A upstream_gene_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918222 p.Gly95Arg missense_variant 0.1
ndh 2102074 p.Met323Lys missense_variant 0.11
PPE35 2168149 p.Pro822Ser missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.32
PPE35 2170053 p.Thr187Ser missense_variant 0.3
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518606 c.492G>C synonymous_variant 0.12
kasA 2518609 p.Met165Ile missense_variant 0.12
fprA 3474914 p.Ala303Val missense_variant 0.13
fprA 3474941 p.Glu312Gly missense_variant 0.11
fbiB 3640974 c.-561T>G upstream_gene_variant 1.0
fbiB 3642192 p.Phe220Ile missense_variant 0.11
embC 4241699 p.Met613Val missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.11
embB 4246548 p.Pro12Gln missense_variant 0.1
embB 4249010 c.2497C>T synonymous_variant 0.1
ethA 4327378 p.Tyr32* stop_gained 1.0
whiB6 4338234 c.288A>G synonymous_variant 1.0
whiB6 4338289 p.Gly78Val missense_variant 0.17
whiB6 4338320 p.Glu68Lys missense_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0