TB-Profiler result

Run: ERR4972474
Summary

Run ID: ERR4972474

Sample name:

Date: 01-04-2023 21:42:51

Number of reads: 7112861

Percentage reads mapped: 99.51

Strain: lineage4.3.2

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
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.2 Euro-American (LAM) LAM3 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
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.13 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288930 p.Ser104Arg missense_variant 1.0 pyrazinamide
ald 3087252 c.436_437dupGC frameshift_variant 0.17 cycloserine
embB 4248003 p.Gln497Arg missense_variant 1.0 ethambutol
gid 4407967 p.Leu79Ser missense_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 7615 p.Leu105Arg missense_variant 0.9
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490757 c.-26T>A upstream_gene_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.25
rpoC 764995 c.1626C>G synonymous_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
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2170065 p.Ala183Gly missense_variant 0.19
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
folC 2747196 p.Asp135Asn missense_variant 0.89
folC 2747490 p.Arg37Cys missense_variant 0.14
pepQ 2860159 p.Ala87Gly missense_variant 0.2
Rv2752c 3065953 p.Thr80Ile missense_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087658 c.840dupG frameshift_variant 0.88
fbiD 3339734 p.Ala206Gly missense_variant 0.47
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
rpoA 3878626 c.-119A>G upstream_gene_variant 0.12
rpoA 3878630 c.-124delC upstream_gene_variant 0.12
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embC 4242402 p.Arg847His missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246584 p.Arg24Pro missense_variant 0.27
ethA 4327378 p.Tyr32* stop_gained 0.99
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0