TB-Profiler result

Run: ERR1950064
Summary

Run ID: ERR1950064

Sample name:

Date: 31-03-2023 15:38:55

Number of reads: 674010

Percentage reads mapped: 99.78

Strain: lineage4

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
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
pncA 2289052 c.185_189delCGGAC frameshift_variant 0.14 pyrazinamide
pncA 2289067 p.Ser59Pro missense_variant 0.13 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 7738 p.Asp146Val missense_variant 0.11
fgd1 491557 p.Lys259Glu missense_variant 0.18
mshA 575704 c.357T>C synonymous_variant 0.12
mshA 576038 p.Asp231Asn missense_variant 0.15
mshA 576373 c.1026G>A synonymous_variant 0.12
mshA 576429 p.Glu361Val missense_variant 0.22
ccsA 620498 p.Leu203Arg missense_variant 0.5
rpoB 759639 c.-168G>C upstream_gene_variant 0.12
rpoB 759812 c.6A>G synonymous_variant 0.15
rpoB 760966 p.Met387Thr missense_variant 0.14
rpoB 763219 p.Ala1138Glu missense_variant 0.2
rpoC 763899 p.Leu177Arg missense_variant 0.17
rpoC 764609 p.Arg414Gly missense_variant 0.33
rpoC 765646 c.2277G>A synonymous_variant 0.12
rpoC 766518 p.Thr1050Ser missense_variant 0.12
rpoC 766633 c.3264G>T synonymous_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776952 p.Leu510Pro missense_variant 0.11
mmpL5 777514 p.Cys323Gly missense_variant 0.12
mmpL5 778216 p.Ser89Arg missense_variant 0.11
mmpL5 778933 c.-453G>T upstream_gene_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781551 c.-9A>C upstream_gene_variant 0.13
rplC 800718 c.-91G>A upstream_gene_variant 0.11
fbiC 1303582 p.Thr218Ala missense_variant 0.15
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1303814 p.Phe295Tyr missense_variant 0.17
fbiC 1303981 p.Val351Ile missense_variant 0.12
fbiC 1304014 p.Pro362Thr missense_variant 0.17
fbiC 1304657 p.Ala576Asp missense_variant 0.14
fbiC 1304949 c.2019C>T synonymous_variant 0.17
embR 1417042 c.306G>A synonymous_variant 0.22
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.12
rrs 1473223 n.1378G>A non_coding_transcript_exon_variant 0.22
rrl 1473922 n.265A>G non_coding_transcript_exon_variant 0.1
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1475067 n.1410A>G non_coding_transcript_exon_variant 0.29
fabG1 1673531 p.Ile31Ser missense_variant 0.18
fabG1 1674105 p.Ser222Arg missense_variant 0.14
inhA 1674351 p.Ile50Met missense_variant 0.17
inhA 1674404 p.Glu68Gly missense_variant 0.25
inhA 1674445 p.Ile82Val missense_variant 0.2
inhA 1674512 p.Gly104Val missense_variant 0.18
inhA 1674723 c.522C>T synonymous_variant 0.13
inhA 1674847 p.Gln216* stop_gained 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102362 c.681G>A synonymous_variant 0.11
katG 2154432 c.1680C>G synonymous_variant 0.12
katG 2154686 p.Ala476Thr missense_variant 0.12
katG 2154792 c.1320T>C synonymous_variant 0.11
katG 2155285 p.His276Arg missense_variant 0.2
PPE35 2168280 p.Pro778Gln missense_variant 0.18
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2168789 c.1824C>T synonymous_variant 0.17
PPE35 2169071 c.1542A>T synonymous_variant 0.29
PPE35 2169165 p.Pro483Leu missense_variant 0.15
PPE35 2169759 p.Gly285Asp missense_variant 0.2
PPE35 2170311 p.Arg101Leu missense_variant 0.12
Rv1979c 2221952 p.Ala405Pro missense_variant 0.22
Rv1979c 2222171 p.Asp332Asn missense_variant 0.2
Rv1979c 2222917 c.246_247delAA frameshift_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289978 c.-737T>G upstream_gene_variant 0.12
kasA 2518288 c.174C>G synonymous_variant 0.13
kasA 2519360 p.Tyr416His missense_variant 0.11
eis 2715050 p.Gly95Arg missense_variant 0.12
eis 2715503 c.-171G>A upstream_gene_variant 0.13
folC 2746463 p.Leu379Arg missense_variant 0.11
pepQ 2860187 p.Ala78Ser missense_variant 0.2
Rv2752c 3064908 p.Ser428Arg missense_variant 0.11
Rv2752c 3064983 c.1209G>A synonymous_variant 0.15
Rv2752c 3065236 p.Ser319Leu missense_variant 0.17
thyX 3067224 p.Val241Ala missense_variant 0.12
thyA 3074067 c.405C>T synonymous_variant 0.18
thyA 3074472 c.-1C>A upstream_gene_variant 0.15
ald 3086895 c.76C>T synonymous_variant 0.14
ald 3087299 p.Met160Ile missense_variant 0.13
fprA 3474729 c.723G>A synonymous_variant 0.13
fprA 3475053 p.Asn349Lys missense_variant 0.4
fbiB 3641987 c.453C>T synonymous_variant 0.17
fbiB 3642195 p.Gly221Ser missense_variant 0.12
fbiB 3642371 c.837G>A synonymous_variant 0.13
fbiB 3642698 c.1164G>C synonymous_variant 0.15
fbiB 3642814 p.Gly427Val missense_variant 0.14
alr 3840570 p.Val284Glu missense_variant 0.14
alr 3841158 p.Glu88Ala missense_variant 0.12
rpoA 3877670 p.Glu280* stop_gained 0.18
rpoA 3878490 c.18C>G synonymous_variant 0.67
rpoA 3878498 p.Ser4Thr missense_variant 0.5
clpC1 4039013 p.Lys564Asn missense_variant 0.12
clpC1 4039289 c.1416T>C synonymous_variant 0.12
clpC1 4040195 c.510G>T synonymous_variant 0.14
clpC1 4040230 p.Gly156Val missense_variant 0.22
embC 4240370 p.Gly170Arg missense_variant 0.12
embA 4242412 c.-821G>A upstream_gene_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242768 p.Arg969Leu missense_variant 0.18
embA 4243262 c.30C>T synonymous_variant 0.12
embA 4244269 p.Arg346Leu missense_variant 0.14
embA 4244386 c.1158_1159dupGC frameshift_variant 0.18
embA 4244677 p.Ser482Leu missense_variant 0.17
embB 4246613 p.Gly34Arg missense_variant 0.17
embB 4246717 c.204C>T synonymous_variant 0.13
embB 4248816 p.Asp768Val missense_variant 0.11
embB 4249689 p.Arg1059Pro missense_variant 0.12
aftB 4268134 p.Leu235Val missense_variant 0.14
ethA 4326537 p.Val313Met missense_variant 0.12
ethA 4327255 p.Gln73His missense_variant 0.17
ethA 4327282 p.Phe64Leu missense_variant 0.12
ethA 4327506 c.-33A>G upstream_gene_variant 0.18
whiB6 4338225 c.297C>T synonymous_variant 0.2
whiB6 4338344 p.Trp60Arg missense_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408115 p.Gly30Cys missense_variant 0.12
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0