TB-Profiler result

Run: SRR833025
Summary

Run ID: SRR833025

Sample name:

Date: 04-04-2023 20:56:45

Number of reads: 985876

Percentage reads mapped: 95.59

Strain: lineage4.3.3

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
lineage4.3.3 Euro-American (LAM) LAM;T RD115 0.97
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
katG 2155168 p.Ser315Thr missense_variant 0.75 isoniazid
ethA 4327015 c.458dupG frameshift_variant 1.0 ethionamide
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 7493 c.192C>T synonymous_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8040 p.Gly247Ser missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoB 760143 p.Val113Ile missense_variant 0.86
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 766720 p.Asp1117Glu missense_variant 0.23
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776689 p.Trp598Arg missense_variant 1.0
mmpL5 778735 c.-255G>A upstream_gene_variant 0.25
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1305452 p.Gly841Val missense_variant 0.5
Rv1258c 1407438 c.-98G>A upstream_gene_variant 0.29
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.2
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.2
rpsA 1834836 p.Met432Thr missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154692 p.Ser474Ala missense_variant 0.27
katG 2156196 c.-85C>T upstream_gene_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 1.0
ahpC 2726338 p.Val49Gly missense_variant 0.33
folC 2746340 p.Ala420Val missense_variant 1.0
thyA 3073806 c.666C>G synonymous_variant 0.22
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473835 c.-172T>C upstream_gene_variant 0.18
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612290 p.Leu276Pro missense_variant 0.27
alr 3840204 p.Glu406Val missense_variant 0.93
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0