TB-Profiler result

Run: ERR2229138
Summary

Run ID: ERR2229138

Sample name:

Date: 31-03-2023 16:43:47

Number of reads: 620472

Percentage reads mapped: 99.42

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
ethA 4327054 p.Tyr140* stop_gained 0.12 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 6094 c.855C>T synonymous_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
fgd1 490649 c.-134C>T upstream_gene_variant 0.13
fgd1 491012 p.Pro77His missense_variant 0.25
rpoB 760918 p.Arg371His missense_variant 0.12
rpoB 761961 p.Pro719Ser missense_variant 0.15
rpoC 762503 c.-867G>A upstream_gene_variant 0.11
rpoC 763860 p.Asp164Val missense_variant 0.15
rpoC 764214 p.Arg282Gln missense_variant 0.15
rpoC 766958 p.Gly1197Cys missense_variant 0.25
mmpL5 775596 p.Ala962Asp missense_variant 0.22
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801320 p.Gly171Val missense_variant 0.13
fbiC 1302738 c.-193G>A upstream_gene_variant 0.2
fbiC 1303747 p.Thr273Ala missense_variant 1.0
Rv1258c 1406179 p.Val388Leu missense_variant 0.12
Rv1258c 1406306 c.1035C>A synonymous_variant 0.22
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
fabG1 1673346 c.-94C>G upstream_gene_variant 0.11
fabG1 1673357 c.-83G>A upstream_gene_variant 0.18
fabG1 1673359 c.-81T>C upstream_gene_variant 0.18
fabG1 1673361 c.-79C>G upstream_gene_variant 0.18
fabG1 1673380 c.-60C>G upstream_gene_variant 0.28
rpsA 1834633 c.1092A>G synonymous_variant 0.25
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918516 p.Gly193Ser missense_variant 0.15
ndh 2101877 p.Gly389Asp missense_variant 0.18
ndh 2102647 c.396C>T synonymous_variant 0.14
katG 2155143 p.Asn323Lys missense_variant 0.25
katG 2156263 c.-152A>G upstream_gene_variant 0.2
PPE35 2167965 p.Ala883Gly missense_variant 0.12
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.53
PPE35 2170053 p.Thr187Ser missense_variant 0.55
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289939 c.-698G>T upstream_gene_variant 0.22
kasA 2518348 c.234A>T synonymous_variant 0.17
folC 2747147 p.Lys151Arg missense_variant 0.2
pepQ 2860476 c.-58A>G upstream_gene_variant 0.14
whiB7 3568608 c.72T>C synonymous_variant 0.11
Rv3236c 3612670 c.447G>T synonymous_variant 0.22
fbiB 3640617 c.-918G>A upstream_gene_variant 0.15
fbiA 3640870 p.Ala110Ser missense_variant 0.14
alr 3840436 c.985C>T synonymous_variant 0.12
ddn 3986715 c.-129A>T upstream_gene_variant 0.14
clpC1 4039018 p.Ser563Ala missense_variant 0.2
clpC1 4039022 c.1683A>G synonymous_variant 0.22
clpC1 4040057 c.648C>T synonymous_variant 0.13
embC 4241968 c.2106A>G synonymous_variant 0.22
embC 4242166 c.2304G>C synonymous_variant 0.29
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245488 c.2256G>T synonymous_variant 0.12
embB 4246544 p.Thr11Pro missense_variant 0.67
embB 4246548 p.Pro12Gln missense_variant 0.75
embB 4246555 c.42G>C synonymous_variant 1.0
embB 4246556 p.Ala15Pro missense_variant 1.0
embB 4246563 p.Leu17Trp missense_variant 1.0
embB 4246567 c.54G>T synonymous_variant 1.0
embB 4247643 p.Val377Glu missense_variant 0.17
embB 4249311 p.Arg933His missense_variant 0.12
ethR 4326961 c.-588G>C upstream_gene_variant 0.15
ethR 4326964 c.-585G>A upstream_gene_variant 0.15
ethR 4326970 c.-579G>T upstream_gene_variant 0.14
ethA 4327420 p.Ser18Arg missense_variant 0.29
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0