TB-Profiler result

Run: SRR023468
Summary

Run ID: SRR023468

Sample name:

Date: 02-04-2023 14:12:21

Number of reads: 1210849

Percentage reads mapped: 79.42

Strain: lineage4.1.2.1

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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 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
embB 4247702 p.Pro397Thr missense_variant 0.17 ethambutol
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 5773 c.534T>C synonymous_variant 0.17
gyrB 7041 p.Ile601Thr missense_variant 0.11
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9162 p.Pro621Ser missense_variant 0.14
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491058 c.276C>T synonymous_variant 0.18
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 1.0
mshA 576542 p.Ala399Thr missense_variant 0.29
ccsA 620477 p.Phe196Ser missense_variant 0.23
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 761735 c.1929C>A synonymous_variant 0.14
rpoC 763826 p.Ala153Ser missense_variant 0.13
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 766585 c.3216T>G synonymous_variant 0.22
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777582 p.Tyr300Cys missense_variant 0.25
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303446 c.516C>A synonymous_variant 0.15
fbiC 1303923 c.993C>A synonymous_variant 0.25
fbiC 1304493 c.1563C>T synonymous_variant 0.15
fbiC 1305193 p.Gly755Cys missense_variant 0.18
fbiC 1305381 c.2451G>T synonymous_variant 0.22
Rv1258c 1406909 c.432C>A synonymous_variant 0.22
Rv1258c 1407277 p.Gly22Cys missense_variant 0.29
Rv1258c 1407281 c.60C>A synonymous_variant 0.25
embR 1416853 c.495G>T synonymous_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1674475 p.Val92Leu missense_variant 0.14
rpsA 1834769 p.Gln410Lys missense_variant 0.12
katG 2154643 p.Gly490Val missense_variant 0.33
katG 2154847 p.Pro422His missense_variant 0.17
PPE35 2168056 p.Pro853Ser missense_variant 0.18
PPE35 2168486 c.2127C>A synonymous_variant 0.12
PPE35 2170227 p.Asn129Ser missense_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290149 c.-908C>T upstream_gene_variant 0.14
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
kasA 2518320 p.Asp69Val missense_variant 0.33
kasA 2518439 p.Ala109Ser missense_variant 0.12
kasA 2518652 p.His180Asn missense_variant 0.15
eis 2714167 p.Ala389Glu missense_variant 0.13
eis 2715519 c.-187G>T upstream_gene_variant 0.12
folC 2746657 c.942T>A synonymous_variant 0.25
pepQ 2860278 c.141C>G synonymous_variant 0.15
ribD 2986956 p.Trp40Arg missense_variant 0.14
ribD 2987347 p.Pro170Leu missense_variant 0.5
Rv2752c 3064751 p.Arg481Cys missense_variant 1.0
Rv2752c 3064766 p.Thr476Ala missense_variant 0.2
thyX 3068068 c.-123C>T upstream_gene_variant 0.2
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339122 p.Ser2Ile missense_variant 0.22
fbiD 3339743 p.Arg209Leu missense_variant 0.25
Rv3083 3448629 c.126C>A synonymous_variant 0.13
Rv3083 3449096 p.Gly198Val missense_variant 0.29
Rv3083 3449114 p.Ala204Val missense_variant 0.2
Rv3083 3449324 p.Arg274Gln missense_variant 0.17
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612456 c.661C>A synonymous_variant 0.13
fbiA 3640379 c.-164T>C upstream_gene_variant 0.95
fbiB 3641196 c.-339C>A upstream_gene_variant 0.22
alr 3840596 p.Met275Ile missense_variant 0.13
alr 3841043 c.378C>T synonymous_variant 0.33
alr 3841076 c.345G>T synonymous_variant 0.4
rpoA 3877729 p.Ser260Tyr missense_variant 0.13
clpC1 4039875 p.Asn277Ile missense_variant 0.13
clpC1 4040779 c.-75C>T upstream_gene_variant 0.14
embC 4240189 c.327G>T synonymous_variant 0.18
embC 4240208 p.Ala116Ser missense_variant 0.22
embC 4240847 p.Asp329Asn missense_variant 0.2
embC 4242273 p.Gly804Val missense_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4246386 p.Arg1052Ser missense_variant 0.13
embB 4248880 c.2367G>A synonymous_variant 0.13
embB 4249343 p.Val944Phe missense_variant 0.25
aftB 4267605 p.Arg411Leu missense_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408016 p.Asp63Asn missense_variant 0.29
gid 4408020 c.183C>T synonymous_variant 0.25