TB-Profiler result

Run: ERR9030268
Summary

Run ID: ERR9030268

Sample name:

Date: 02-04-2023 09:24:41

Number of reads: 1646209

Percentage reads mapped: 99.96

Strain: lineage4

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
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
katG 2154013 c.2098dupT frameshift_variant 1.0 isoniazid
pncA 2289222 p.Val7Gly missense_variant 1.0 pyrazinamide
ahpC 2726139 c.-54C>T upstream_gene_variant 1.0 isoniazid
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 576637 p.Trp430Cys missense_variant 0.2
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 0.97
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471868 n.23T>G non_coding_transcript_exon_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1475843 n.2186G>T non_coding_transcript_exon_variant 0.12
rrl 1476338 n.2681C>A non_coding_transcript_exon_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1917988 p.Ala17Thr missense_variant 0.18
tlyA 1918117 p.Arg60Cys missense_variant 0.15
PPE35 2168149 p.Pro822Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 0.98
eis 2715053 p.Arg94Ser missense_variant 0.15
pepQ 2859607 p.Arg271Gln missense_variant 0.14
fprA 3475349 p.Ala448Val missense_variant 0.11
clpC1 4039729 p.Asp326Asn missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4247642 p.Val377Leu missense_variant 0.12
embB 4247688 p.Leu392Pro missense_variant 0.2
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0