TB-Profiler result

Run: ERR1034809
Summary

Run ID: ERR1034809

Sample name:

Date: 31-03-2023 09:42:44

Number of reads: 20511965

Percentage reads mapped: 99.63

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 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 1.0 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2154151 c.1953_1960dupGTCACTGA frameshift_variant&stop_gained 0.97 isoniazid
katG 2154166 c.1945dupG frameshift_variant 1.0 isoniazid
pncA 2289016 p.Thr76Pro missense_variant 1.0 pyrazinamide
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
ethA 4326721 c.752dupG frameshift_variant 1.0 ethionamide, 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 575526 p.Pro60Leu 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 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2156384 c.-273G>A upstream_gene_variant 1.0
PPE35 2169320 p.Leu431Phe missense_variant 0.25
PPE35 2169866 c.747G>C synonymous_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ribD 2987176 p.Glu113Gly missense_variant 1.0
thyA 3073806 c.666C>G synonymous_variant 0.18
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
Rv3083 3448500 c.-4A>G upstream_gene_variant 1.0
Rv3083 3448501 c.-3G>T upstream_gene_variant 0.75
alr 3840764 c.657G>C synonymous_variant 1.0
alr 3841362 p.Thr20Met missense_variant 1.0
clpC1 4038857 c.1848C>A synonymous_variant 0.15
embC 4239842 c.-21C>A upstream_gene_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242822 p.Val987Gly missense_variant 0.26
ubiA 4269529 p.Ala102Gly missense_variant 0.17
whiB6 4338420 p.Cys34* stop_gained 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407976 p.Gly76Asp missense_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0