TB-Profiler result

Run: SRR4035860
Summary

Run ID: SRR4035860

Sample name:

Date: 04-04-2023 07:20:36

Number of reads: 842677

Percentage reads mapped: 99.63

Strain: lineage4.3.2.1

Drug-resistance: Other

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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 0.99
lineage4.3.2 Euro-American (LAM) LAM3 None 1.0
lineage4.3.2.1 Euro-American (LAM) LAM3 RD761 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
ethA 4326669 p.Gln269* stop_gained 0.11 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
gyrB 5520 p.Pro94Leu missense_variant 1.0
gyrB 5594 p.Gly119Cys missense_variant 0.12
gyrB 6143 p.His302Asn missense_variant 0.17
gyrA 7222 c.-80C>T upstream_gene_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491289 c.507C>A synonymous_variant 0.15
fgd1 491588 p.Glu269Gly missense_variant 0.14
rpoB 759863 c.57A>G synonymous_variant 0.18
rpoC 763973 p.Glu202* stop_gained 0.17
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpS5 778767 p.Asp47Asn missense_variant 0.18
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304109 c.1179C>T synonymous_variant 0.2
fbiC 1304987 p.Pro686Gln missense_variant 0.2
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 1.0
rrl 1475478 n.1829_1830delAC non_coding_transcript_exon_variant 0.14
fabG1 1673195 c.-245C>T upstream_gene_variant 0.12
inhA 1674410 p.His70Arg missense_variant 0.15
rpsA 1833511 c.-31G>T upstream_gene_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918563 c.624G>A synonymous_variant 0.12
ndh 2102263 p.Lys260Asn missense_variant 0.11
ndh 2102940 p.Arg35Trp missense_variant 0.12
katG 2155442 p.Gln224* stop_gained 0.12
katG 2155964 p.Gln50Lys missense_variant 0.11
katG 2156118 c.-7G>T upstream_gene_variant 0.11
PPE35 2169866 c.747G>C synonymous_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
thyA 3073806 c.666C>G synonymous_variant 0.12
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
alr 3840365 c.1056C>G synonymous_variant 0.17
alr 3840839 p.Met194Ile missense_variant 0.15
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embC 4240555 p.Met231Ile missense_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243605 p.Val125Leu missense_variant 0.12
embB 4247160 p.Thr216Lys missense_variant 0.13
whiB6 4338307 p.Ala72Val missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0