TB-Profiler result

Run: SRR10809051
Summary

Run ID: SRR10809051

Sample name:

Date: 02-04-2023 19:20:48

Number of reads: 2994698

Percentage reads mapped: 99.61

Strain: lineage4.9;lineage4.3

Drug-resistance: HR-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 0.13
lineage4.9 Euro-American (H37Rv-like) T1 None 0.85
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
fabG1 1673425 c.-15C>T upstream_gene_variant 0.22 isoniazid, ethionamide
pncA 2288997 p.His82Arg missense_variant 0.14 pyrazinamide
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 0.12
gyrA 9074 c.1773G>A synonymous_variant 0.16
gyrA 9304 p.Gly668Asp missense_variant 0.11
mshA 576108 p.Ala254Gly missense_variant 0.27
rpoC 764995 c.1626C>G synonymous_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777182 c.1299C>T synonymous_variant 0.83
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406785 p.Leu186Phe missense_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472179 n.334C>T non_coding_transcript_exon_variant 0.16
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154350 p.Glu588Lys missense_variant 0.86
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv2752c 3066335 c.-144T>G upstream_gene_variant 0.16
ald 3086788 c.-32T>C upstream_gene_variant 0.21
Rv3236c 3612176 p.Arg314Gln missense_variant 0.15
alr 3841612 c.-193_-192insC upstream_gene_variant 0.81
clpC1 4038287 c.2418C>T synonymous_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243081 c.-152T>G upstream_gene_variant 0.81
embB 4246584 p.Arg24Pro missense_variant 0.18
ethA 4326423 p.Gly351Trp missense_variant 0.87
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 0.25