TB-Profiler result

Run: ERR2229650
Summary

Run ID: ERR2229650

Sample name:

Date: 31-03-2023 17:23:40

Number of reads: 551632

Percentage reads mapped: 99.27

Strain: lineage4.8

Drug-resistance: Sensitive

Download CSV Download TXT Download PDF Download JSON
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 6055 p.His272Gln missense_variant 0.13
gyrA 6896 c.-406C>A upstream_gene_variant 0.19
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 9584 p.Arg761Ser missense_variant 0.17
fgd1 491339 p.Gly186Val missense_variant 0.18
fgd1 491372 p.Gly197Ala missense_variant 0.22
fgd1 491466 p.Met228Ile missense_variant 0.33
ccsA 620794 c.906delC frameshift_variant 0.14
rpoB 760164 p.Asp120Tyr missense_variant 0.12
rpoB 761286 p.Leu494Met missense_variant 0.17
rpoB 761754 p.Asp650Tyr missense_variant 0.15
rpoB 762356 p.Glu850Asp missense_variant 0.17
rpoC 763483 c.114G>T synonymous_variant 0.18
rpoC 764267 p.Ala300Ser missense_variant 0.22
rpoC 764405 p.Arg346Trp missense_variant 0.13
rpoC 764617 c.1248C>T synonymous_variant 0.11
rpoC 765464 p.Asp699Asn missense_variant 0.15
rpoC 767163 p.Asn1265Ser missense_variant 0.22
mmpL5 775633 p.Gln950* stop_gained 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775973 p.Leu836Phe missense_variant 0.4
mmpL5 776061 p.Thr807Asn missense_variant 0.15
mmpL5 776371 p.Gly704Cys missense_variant 0.17
mmpL5 776858 p.Ser541Arg missense_variant 0.18
mmpS5 778656 p.Ala84Ser missense_variant 0.13
mmpR5 779326 p.Glu113* stop_gained 0.17
mmpS5 779576 c.-671C>A upstream_gene_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302811 c.-120G>T upstream_gene_variant 0.25
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304764 p.Thr612Ala missense_variant 0.11
fbiC 1305152 p.Pro741Leu missense_variant 0.12
Rv1258c 1406504 c.837C>A synonymous_variant 0.2
atpE 1460883 c.-162G>T upstream_gene_variant 0.25
atpE 1461009 c.-36G>T upstream_gene_variant 0.2
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474276 n.619C>T non_coding_transcript_exon_variant 0.14
rrl 1474708 n.1051C>A non_coding_transcript_exon_variant 0.18
rrl 1474768 n.1111C>A non_coding_transcript_exon_variant 0.18
fabG1 1673346 c.-94C>G upstream_gene_variant 0.14
fabG1 1673349 c.-91G>C upstream_gene_variant 0.2
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
rpsA 1834301 p.Val254Phe missense_variant 0.14
rpsA 1834703 p.Gly388Arg missense_variant 0.22
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918030 p.Lys31Glu missense_variant 0.22
ndh 2102653 p.His130Glu missense_variant 0.14
ndh 2103078 c.-36C>A upstream_gene_variant 0.14
ndh 2103142 c.-100A>T upstream_gene_variant 0.18
PPE35 2167814 c.2799C>T synonymous_variant 0.27
PPE35 2167965 p.Ala883Gly missense_variant 0.15
PPE35 2167967 c.2646A>C synonymous_variant 0.15
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2168970 p.Ile548Asn missense_variant 0.2
PPE35 2169044 c.1569G>C synonymous_variant 0.22
PPE35 2169269 c.1344A>G synonymous_variant 0.2
PPE35 2169272 c.1341C>G synonymous_variant 0.19
PPE35 2169732 p.Asn294Ser missense_variant 0.15
PPE35 2169902 p.Leu237Phe missense_variant 0.2
PPE35 2169910 p.Asn235Tyr missense_variant 0.18
PPE35 2170048 p.Leu189Val missense_variant 0.49
PPE35 2170053 p.Thr187Ser missense_variant 0.5
Rv1979c 2222580 c.585G>T synonymous_variant 0.13
Rv1979c 2222676 c.489C>T synonymous_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289617 c.-376G>A upstream_gene_variant 0.13
pncA 2289681 c.-440T>C upstream_gene_variant 0.12
pncA 2289690 c.-449A>G upstream_gene_variant 0.11
pncA 2289957 c.-716G>T upstream_gene_variant 0.12
pncA 2290057 c.-816G>T upstream_gene_variant 0.12
kasA 2518082 c.-33C>A upstream_gene_variant 0.15
eis 2714466 p.Trp289Cys missense_variant 0.12
eis 2714581 p.Ala251Glu missense_variant 0.17
ahpC 2726332 p.Trp47* stop_gained 0.14
folC 2747097 p.Val168Ile missense_variant 0.15
pepQ 2860481 c.-63C>T upstream_gene_variant 0.18
ribD 2986817 c.-22G>T upstream_gene_variant 0.12
ribD 2986896 p.Val20Met missense_variant 0.13
ribD 2987526 p.Gly230Arg missense_variant 0.18
Rv2752c 3065462 p.Arg244Trp missense_variant 0.15
thyX 3067984 c.-39C>A upstream_gene_variant 0.2
thyA 3073917 c.555C>A synonymous_variant 0.15
thyA 3074602 c.-131G>T upstream_gene_variant 0.12
ald 3087114 p.Ala99Pro missense_variant 0.11
ald 3087493 p.Leu225Pro missense_variant 0.18
ald 3087671 p.Asp284Glu missense_variant 0.14
fprA 3475224 c.1218G>T synonymous_variant 0.14
whiB7 3568762 c.-83G>T upstream_gene_variant 0.17
Rv3236c 3612868 c.249C>A synonymous_variant 0.18
fbiA 3640904 p.Ala121Asp missense_variant 0.33
fbiB 3641878 p.Arg115Gln missense_variant 0.17
fbiB 3642731 c.1197C>A synonymous_variant 0.2
alr 3841129 c.292C>T synonymous_variant 1.0
alr 3841546 c.-126C>A upstream_gene_variant 0.43
rpoA 3878462 p.Asp16His missense_variant 0.25
clpC1 4039417 p.Glu430* stop_gained 0.4
clpC1 4039645 p.His354Asp missense_variant 0.2
clpC1 4039959 p.Thr249Lys missense_variant 0.13
clpC1 4040144 c.561G>C synonymous_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242817 p.Trp985Cys missense_variant 0.12
embB 4246737 p.Thr75Lys missense_variant 0.22
embB 4249277 p.Tyr922Asn missense_variant 0.12
aftB 4268050 p.Pro263Thr missense_variant 0.18
aftB 4268235 p.Leu201Ser missense_variant 0.17
ethA 4326951 p.Ala175Ser missense_variant 0.17
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
ethR 4327693 p.Asp49Tyr missense_variant 0.2
ethR 4327807 p.Leu87Ile missense_variant 0.25
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407925 p.Pro93Gln missense_variant 0.13
Rv3083 3448497 c.-6_*1408del transcript_ablation 1.0