TB-Profiler result

Run: ERR7911359
Summary

Run ID: ERR7911359

Sample name:

Date: 02-04-2023 06:57:35

Number of reads: 677409

Percentage reads mapped: 99.65

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 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.3 Euro-American (LAM) LAM;T RD115 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
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
gid 4408068 p.Trp45* stop_gained 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
gyrB 5705 p.Leu156Met missense_variant 0.11
gyrA 7362 p.Glu21Gln missense_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
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
rrl 1474357 n.700G>T non_coding_transcript_exon_variant 0.4
rrl 1476502 n.2845G>A non_coding_transcript_exon_variant 0.29
inhA 1674522 c.321G>T synonymous_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169013 p.Val534Leu missense_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289913 c.-672T>A upstream_gene_variant 0.4
kasA 2518919 p.Gly269Ser missense_variant 1.0
folC 2747032 c.567A>G synonymous_variant 0.1
thyX 3067499 p.Lys149Asn missense_variant 0.18
thyX 3067939 p.Glu3Lys missense_variant 0.17
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086844 p.Thr9Ala missense_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612483 p.His212Asn missense_variant 0.21
rpoA 3878148 p.Asn120Lys missense_variant 0.12
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embC 4242182 p.Ala774Ser missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
aftB 4266961 c.1876C>A synonymous_variant 0.15
aftB 4266969 p.Pro623Gln missense_variant 0.13
aftB 4267895 p.Phe314Leu missense_variant 0.33
aftB 4267899 p.Ala313Asp missense_variant 0.18
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338600 c.-79T>C upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0