TB-Profiler result

Run: ERR2229343
Summary

Run ID: ERR2229343

Sample name:

Date: 31-03-2023 17:04:49

Number of reads: 1420281

Percentage reads mapped: 98.98

Strain: lineage4.8

Drug-resistance: Sensitive

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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
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 6399 p.Val387Ala missense_variant 0.15
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 9252 p.Val651Ile missense_variant 0.15
mshA 576108 p.Ala254Gly missense_variant 0.22
ccsA 620262 c.372C>T synonymous_variant 0.15
ccsA 620268 c.378G>T synonymous_variant 0.15
ccsA 620438 p.Ser183Tyr missense_variant 0.12
ccsA 620472 p.Ile194Met missense_variant 0.14
rpoC 764233 c.866delA frameshift_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776145 p.Ala779Asp missense_variant 0.21
mmpL5 778086 c.394delG frameshift_variant 0.15
mmpS5 779597 c.-693delA upstream_gene_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
Rv1258c 1406353 p.Pro330Thr missense_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472208 n.363A>G non_coding_transcript_exon_variant 0.11
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.14
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1475467 n.1810G>T non_coding_transcript_exon_variant 0.18
fabG1 1673357 c.-83G>A upstream_gene_variant 0.12
fabG1 1673359 c.-81T>C upstream_gene_variant 0.12
fabG1 1673361 c.-79C>G upstream_gene_variant 0.12
fabG1 1673380 c.-60C>G upstream_gene_variant 0.35
fabG1 1674178 c.740delA frameshift_variant 0.15
inhA 1674948 p.Trp249* stop_gained 0.14
rpsA 1833355 c.-187C>A upstream_gene_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102714 c.328delA frameshift_variant 0.12
katG 2153970 p.Asp714Glu missense_variant 0.21
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169278 c.1335T>C synonymous_variant 0.28
PPE35 2169281 c.1332T>G synonymous_variant 0.28
PPE35 2169287 c.1326T>C synonymous_variant 0.31
PPE35 2169488 c.1125G>C synonymous_variant 0.12
PPE35 2169491 c.1122T>C synonymous_variant 0.12
PPE35 2170048 p.Leu189Val missense_variant 0.7
PPE35 2170053 p.Thr187Ser missense_variant 0.72
PPE35 2170371 p.Thr81Val missense_variant 0.13
PPE35 2170392 p.Gly74Ala missense_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518197 p.Asp28Ala missense_variant 0.17
kasA 2518200 p.Ile29Asn missense_variant 0.17
kasA 2518201 c.88delG frameshift_variant 0.18
kasA 2518218 p.Gly35Ala missense_variant 0.19
kasA 2518226 p.Ala38Ser missense_variant 0.21
kasA 2518864 c.750G>C synonymous_variant 0.19
kasA 2519187 p.Thr358Met missense_variant 0.18
kasA 2519330 p.Gly406Ser missense_variant 0.12
Rv2752c 3066081 c.111G>T synonymous_variant 0.22
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
Rv3083 3448500 c.-4A>G upstream_gene_variant 1.0
Rv3083 3448501 c.-3G>T upstream_gene_variant 1.0
whiB7 3568418 c.250_261delGGACGTCCGCGC conservative_inframe_deletion 0.12
fbiB 3642673 p.Ala380Gly missense_variant 0.17
alr 3841546 c.-126C>A upstream_gene_variant 0.24
rpoA 3878599 c.-92C>G upstream_gene_variant 0.67
clpC1 4039071 p.Pro545Gln missense_variant 0.15
clpC1 4039508 c.1197G>C synonymous_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242686 p.Gln942Lys missense_variant 0.4
embA 4244184 p.Ser318Arg missense_variant 0.15
embA 4244522 c.1290C>A synonymous_variant 0.2
embB 4246283 c.-231G>A upstream_gene_variant 0.18
embB 4246544 p.Thr11Pro missense_variant 0.24
embB 4246548 p.Pro12Gln missense_variant 0.62
embB 4246555 c.42G>C synonymous_variant 0.58
embB 4246556 p.Ala15Pro missense_variant 0.58
embB 4246567 c.54_55insT frameshift_variant 0.25
ethR 4326964 c.-585G>A upstream_gene_variant 0.13
ethR 4326970 c.-579G>T upstream_gene_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0