TB-Profiler result

Run: ERR2229090
Summary

Run ID: ERR2229090

Sample name:

Date: 31-03-2023 16:37:47

Number of reads: 698270

Percentage reads mapped: 99.46

Strain: lineage4.8

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
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 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
tlyA 1918517 c.582delC frameshift_variant 0.12 capreomycin
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 7398 p.Met33Leu missense_variant 0.13
mshA 575862 p.Pro172Gln missense_variant 0.11
mshA 576108 p.Ala254Gly missense_variant 0.2
mshA 576114 p.Arg256Pro missense_variant 0.22
rpoB 759914 c.108T>C synonymous_variant 0.1
rpoB 761569 p.Ile588Asn missense_variant 0.18
rpoB 761926 p.Met707Thr missense_variant 0.12
rpoC 763551 p.Tyr61Cys missense_variant 0.1
rpoC 765262 c.1893C>G synonymous_variant 0.12
rpoC 766345 c.2976T>C synonymous_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776032 p.Gly817Trp missense_variant 0.2
mmpL5 776751 p.Phe577Tyr missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303367 p.Thr146Asn missense_variant 0.12
fbiC 1303681 c.751T>C synonymous_variant 0.25
fbiC 1303747 p.Thr273Ala missense_variant 1.0
embR 1416565 p.Asp261Glu missense_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473029 n.1184C>T non_coding_transcript_exon_variant 0.22
rrl 1473498 n.-160G>T upstream_gene_variant 0.18
rrl 1473714 n.57C>T non_coding_transcript_exon_variant 0.33
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
fabG1 1673416 c.-24G>A upstream_gene_variant 0.17
rpsA 1833526 c.-16G>T upstream_gene_variant 0.12
rpsA 1834052 p.Ala171Ser missense_variant 0.12
tlyA 1917941 p.Val1Ala missense_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918205 p.Ala89Glu missense_variant 0.15
ndh 2102188 c.855G>A synonymous_variant 0.2
ndh 2103056 c.-14A>T upstream_gene_variant 0.18
PPE35 2167973 c.2640A>G synonymous_variant 0.11
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.5
PPE35 2170053 p.Thr187Ser missense_variant 0.53
PPE35 2170238 c.375T>G synonymous_variant 0.12
Rv1979c 2222243 p.Ala308Ser missense_variant 0.15
Rv1979c 2222286 c.879G>T synonymous_variant 0.17
Rv1979c 2222876 c.288delC frameshift_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289239 c.3G>A start_lost 0.13
kasA 2518445 p.Val111Ile missense_variant 0.13
kasA 2518606 c.492G>C synonymous_variant 0.2
kasA 2518609 p.Met165Ile missense_variant 0.2
kasA 2519153 p.Ile347Val missense_variant 0.18
pepQ 2860226 p.Ala65Ser missense_variant 0.17
pepQ 2860584 c.-166C>T upstream_gene_variant 0.17
pepQ 2860601 c.-183C>A upstream_gene_variant 0.12
ribD 2987136 p.Val100Ile missense_variant 0.14
Rv2752c 3065419 p.Arg258Leu missense_variant 0.15
alr 3840533 c.888G>T synonymous_variant 0.15
rpoA 3877572 c.936G>T synonymous_variant 0.13
clpC1 4038301 p.Val802Ile missense_variant 0.12
clpC1 4039162 p.His515Asn missense_variant 0.13
embC 4241143 c.1281C>A synonymous_variant 0.13
embC 4241960 c.2098C>T synonymous_variant 0.29
embC 4242086 p.Gln742* stop_gained 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244144 c.912C>T synonymous_variant 0.18
embB 4246196 c.-318C>T upstream_gene_variant 0.22
embB 4246555 c.42G>C synonymous_variant 0.5
embB 4246556 p.Ala15Pro missense_variant 0.5
embB 4246563 p.Leu17Trp missense_variant 0.5
embB 4246567 c.54G>T synonymous_variant 0.5
ethR 4326961 c.-588G>C upstream_gene_variant 0.14
ethR 4326964 c.-585G>A upstream_gene_variant 0.14
ethR 4326970 c.-579G>T upstream_gene_variant 0.14
ethA 4327483 c.-10G>T upstream_gene_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0