TB-Profiler result

Run: ERR2229057
Summary

Run ID: ERR2229057

Sample name:

Date: 31-03-2023 16:33:40

Number of reads: 466735

Percentage reads mapped: 98.71

Strain: lineage4

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
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 2155193 p.Gly307Arg missense_variant 0.5 isoniazid
pncA 2288730 p.Ala171Glu missense_variant 0.17 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
gyrB 5856 p.Ile206Asn missense_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
mshA 575341 c.-7T>C upstream_gene_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.5
rpoB 759764 c.-43T>A upstream_gene_variant 0.22
rpoC 763316 c.-54T>C upstream_gene_variant 0.13
rpoC 763934 p.Ala189Ser missense_variant 0.15
rpoC 765939 p.Arg857Leu missense_variant 0.25
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
atpE 1460999 c.-46C>A upstream_gene_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471806 n.-40T>C upstream_gene_variant 0.18
rrs 1473161 n.1316A>C non_coding_transcript_exon_variant 0.14
rrs 1473164 n.1319C>A non_coding_transcript_exon_variant 0.14
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.15
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.15
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.15
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.14
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1475326 n.1669A>C non_coding_transcript_exon_variant 0.17
rrl 1476639 n.2982G>A non_coding_transcript_exon_variant 0.29
fabG1 1673200 c.-240C>T upstream_gene_variant 0.14
fabG1 1673380 c.-60C>G upstream_gene_variant 0.22
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155520 p.Trp198Arg missense_variant 0.14
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169127 p.Val496Ile missense_variant 0.18
PPE35 2169269 c.1344A>G synonymous_variant 0.13
PPE35 2169272 c.1341C>G synonymous_variant 0.14
PPE35 2169278 c.1335T>C synonymous_variant 0.17
PPE35 2169281 c.1332T>G synonymous_variant 0.18
PPE35 2169287 c.1326T>C synonymous_variant 0.17
PPE35 2169293 c.1320T>C synonymous_variant 0.17
PPE35 2169308 c.1305C>T synonymous_variant 0.22
PPE35 2169717 p.Asn299Ile missense_variant 0.15
PPE35 2169725 c.888T>C synonymous_variant 0.11
PPE35 2169902 p.Leu237Phe missense_variant 0.2
PPE35 2170048 p.Leu189Val missense_variant 0.4
PPE35 2170053 p.Thr187Ser missense_variant 0.44
PPE35 2170244 c.369G>A synonymous_variant 0.15
PPE35 2170249 p.Ile122Leu missense_variant 0.14
PPE35 2170298 c.315A>G synonymous_variant 0.14
PPE35 2170308 p.Leu102Ala missense_variant 0.17
PPE35 2170313 c.300G>C synonymous_variant 0.15
Rv1979c 2222940 c.224delA frameshift_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv2752c 3064740 c.1452C>A synonymous_variant 0.22
thyA 3073974 c.498C>T synonymous_variant 0.2
ald 3086703 c.-117T>C upstream_gene_variant 0.12
embC 4241416 c.1554C>T synonymous_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.6
embB 4246747 p.Asp78Glu missense_variant 0.27
embB 4247964 p.Ala484Asp missense_variant 0.17
embB 4248053 p.Pro514Ser missense_variant 0.29
embB 4249629 p.Ile1039Asn missense_variant 0.2
aftB 4267205 c.1632G>A synonymous_variant 0.17
aftB 4269066 c.-230C>A upstream_gene_variant 0.17
ubiA 4269967 c.-134C>T upstream_gene_variant 0.18
ethR 4327760 p.Val71Glu missense_variant 0.21
whiB6 4338589 c.-68G>T upstream_gene_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407605 p.Ala200Thr missense_variant 0.22
Rv3083 3448497 c.-6_*1408del transcript_ablation 1.0