TB-Profiler result

Run: ERR2229535

Summary

Run ID: ERR2229535

Sample name:

Date: 31-03-2023 17:17:39

Number of reads: 609230

Percentage reads mapped: 99.36

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 5984 p.Arg249Ser missense_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
fgd1 490744 c.-39T>C upstream_gene_variant 0.12
fgd1 491129 p.Thr116Asn missense_variant 0.18
mshA 575924 p.Gly193* stop_gained 0.25
mshA 576080 p.Asp245His missense_variant 0.4
ccsA 620624 p.Ile245Lys missense_variant 0.14
rpoB 761289 p.Ser495Ala missense_variant 0.33
rpoB 761297 p.Tyr497* stop_gained 0.4
rpoB 761516 c.1710G>T synonymous_variant 0.17
rpoB 761879 p.Glu691Asp missense_variant 0.18
rpoB 762285 p.Arg827Cys missense_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777125 p.Ser452Arg missense_variant 0.14
mmpL5 777157 c.1324C>A synonymous_variant 0.2
mmpL5 777164 c.1317C>T synonymous_variant 0.18
mmpL5 778431 p.Arg17Thr missense_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801278 p.Pro157Leu missense_variant 0.2
fbiC 1302764 c.-167A>G upstream_gene_variant 0.12
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304301 c.1371C>A synonymous_variant 0.22
Rv1258c 1406502 p.Val280Ala missense_variant 0.2
Rv1258c 1406931 p.Trp137Leu missense_variant 0.2
Rv1258c 1407089 c.252G>T synonymous_variant 0.29
embR 1417525 c.-178G>C upstream_gene_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473058 n.1213G>A non_coding_transcript_exon_variant 0.29
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1476006 n.2349G>A non_coding_transcript_exon_variant 0.22
rrl 1476705 n.3048C>T non_coding_transcript_exon_variant 0.22
fabG1 1673346 c.-94C>G upstream_gene_variant 0.16
fabG1 1673349 c.-91G>C upstream_gene_variant 0.17
fabG1 1673357 c.-83G>A upstream_gene_variant 0.22
fabG1 1673359 c.-81T>C upstream_gene_variant 0.23
fabG1 1673361 c.-79C>G upstream_gene_variant 0.23
fabG1 1673380 c.-60C>G upstream_gene_variant 0.28
fabG1 1674157 p.Asp240Tyr missense_variant 0.15
rpsA 1834205 p.Phe222Ile missense_variant 0.25
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918592 p.Leu218Pro missense_variant 0.15
ndh 2102584 p.Ser153Arg missense_variant 0.17
ndh 2103186 c.-144T>C upstream_gene_variant 0.11
katG 2155647 c.465C>T synonymous_variant 0.18
katG 2155729 p.Arg128Gln missense_variant 0.29
PPE35 2167814 c.2799C>T synonymous_variant 0.21
PPE35 2167868 c.2745A>C synonymous_variant 0.11
PPE35 2168165 c.2448G>C synonymous_variant 0.29
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.38
PPE35 2170053 p.Thr187Ser missense_variant 0.33
Rv1979c 2221950 c.1215T>C synonymous_variant 0.14
Rv1979c 2222451 c.714C>T synonymous_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288701 p.Glu181Lys missense_variant 0.22
pncA 2288712 p.Thr177Ile missense_variant 0.2
pncA 2289380 c.-139G>T upstream_gene_variant 0.25
pncA 2290076 c.-835C>A upstream_gene_variant 0.12
kasA 2518394 p.Leu94Ile missense_variant 0.14
kasA 2518809 p.Lys232Arg missense_variant 0.25
eis 2715210 c.123C>A synonymous_variant 0.11
ahpC 2726450 c.258G>A synonymous_variant 0.15
ahpC 2726757 p.Glu189* stop_gained 0.12
folC 2746456 c.1143G>A synonymous_variant 0.25
thyX 3067958 c.-13T>C upstream_gene_variant 0.29
ald 3086974 p.Ala52Val missense_variant 0.12
Rv3236c 3612741 p.Tyr126His missense_variant 0.12
fbiA 3640448 c.-95A>T upstream_gene_variant 0.2
fbiA 3640480 c.-63C>A upstream_gene_variant 0.18
fbiB 3641871 p.Val113Ile missense_variant 0.18
clpC1 4039418 c.1287C>T synonymous_variant 0.17
clpC1 4039645 p.His354Asp missense_variant 0.2
clpC1 4039654 p.Thr351Ser missense_variant 0.2
clpC1 4040144 c.561G>C synonymous_variant 0.15
embC 4239691 c.-172G>T upstream_gene_variant 0.12
embC 4240409 p.Pro183Ala missense_variant 0.18
embC 4242047 p.Ser729Pro missense_variant 0.33
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242704 p.Asp948Asn missense_variant 0.17
embB 4245563 c.-951G>T upstream_gene_variant 0.17
embB 4246082 c.-432T>C upstream_gene_variant 0.2
embB 4246555 c.42G>C synonymous_variant 0.5
embB 4246556 p.Ala15Pro missense_variant 0.5
embB 4246563 p.Leu17Trp missense_variant 0.33
embB 4247601 p.Leu363Arg missense_variant 0.14
aftB 4266972 p.Gly622Asp missense_variant 0.25
aftB 4267135 p.Cys568Arg missense_variant 0.15
aftB 4267303 p.Asn512Asp missense_variant 0.12
ubiA 4269969 c.-136G>T upstream_gene_variant 0.12
ethA 4327382 p.Ser31Ile missense_variant 0.18
ethA 4327771 c.-298G>A upstream_gene_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448497 c.-6_*1408del transcript_ablation 1.0