TB-Profiler result

Run: ERR2516434
Summary

Run ID: ERR2516434

Sample name:

Date: 31-03-2023 21:32:14

Number of reads: 3542356

Percentage reads mapped: 99.72

Strain: lineage4.1.4

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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.4 Euro-American T;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 761139 p.His445Cys missense_variant 1.0 rifampicin
rrs 1473247 n.1402C>T non_coding_transcript_exon_variant 1.0 kanamycin, capreomycin, aminoglycosides, amikacin
inhA 1674481 p.Ser94Ala missense_variant 0.97 isoniazid, ethionamide
katG 2155212 p.Trp300* stop_gained 0.98 isoniazid
pncA 2288859 p.Val128Gly missense_variant 1.0 pyrazinamide
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
gid 4408087 c.115delC frameshift_variant 1.0 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
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoB 761559 p.Thr585Ala missense_variant 1.0
rpoC 765150 p.Gly594Glu missense_variant 0.99
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 778042 p.Ala147Thr missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471861 n.16T>C non_coding_transcript_exon_variant 1.0
rrs 1473235 n.1390C>T non_coding_transcript_exon_variant 1.0
rrl 1474939 n.1282C>A non_coding_transcript_exon_variant 0.11
rrl 1475164 n.1507C>T non_coding_transcript_exon_variant 0.11
rrl 1476029 n.2372A>G non_coding_transcript_exon_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168298 p.Pro772Leu missense_variant 1.0
PPE35 2169320 p.Leu431Phe missense_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv2752c 3066058 p.Cys45Tyr missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 0.98
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embB 4249408 c.2895G>A synonymous_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0