TB-Profiler result

Run: SRR22175241
Summary

Run ID: SRR22175241

Sample name:

Date: 04-04-2023 04:02:30

Number of reads: 1226635

Percentage reads mapped: 99.48

Strain: lineage4.3

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 0.95
lineage4.3 Euro-American (LAM) mainly-LAM None 0.91
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
fabG1 1673432 c.-8T>C upstream_gene_variant 0.92 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288718 c.523delA frameshift_variant 1.0 pyrazinamide
embA 4243217 c.-16C>T upstream_gene_variant 0.92 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
gyrA 7581 p.Asp94Arg missense_variant 0.88
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoB 759836 c.30C>G synonymous_variant 0.1
rpoC 764995 c.1626C>G synonymous_variant 0.87
rpoC 765570 p.Ala734Val missense_variant 0.91
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776203 p.Gly760Cys missense_variant 0.12
mmpS5 779561 c.-656C>T upstream_gene_variant 0.12
mmpS5 779670 c.-765A>G upstream_gene_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473022 n.1177G>T non_coding_transcript_exon_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 0.88
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
clpC1 4038287 c.2418C>T synonymous_variant 0.92
embA 4242643 c.-590C>T upstream_gene_variant 1.0
ethA 4326296 p.Leu393Arg missense_variant 0.13
ethA 4326676 p.Ser266Arg missense_variant 0.11
ethA 4327269 p.Trp69Arg missense_variant 0.92
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408063 p.Arg47Leu missense_variant 0.97
gid 4408156 p.Leu16Arg missense_variant 0.97
whiB6 4338199 c.-10_322del frameshift_variant&start_lost 1.0