TB-Profiler result

Run: ERR2679270
Summary

Run ID: ERR2679270

Sample name:

Date: 31-03-2023 23:00:45

Number of reads: 310936

Percentage reads mapped: 94.31

Strain: lineage4.1.2

Drug-resistance: HR-TB

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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 0.99
lineage4.1.2 Euro-American T;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
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7622 c.321C>T synonymous_variant 0.12
gyrA 7631 c.330G>C synonymous_variant 0.12
gyrA 7637 c.336C>G synonymous_variant 0.13
gyrA 7652 c.351C>T synonymous_variant 0.13
gyrA 7658 c.357A>G synonymous_variant 0.13
gyrA 7661 c.360C>T synonymous_variant 0.13
gyrA 7664 c.363T>C synonymous_variant 0.13
gyrA 7670 c.369A>G synonymous_variant 0.12
gyrA 7676 c.375G>C synonymous_variant 0.12
gyrA 7679 c.378G>C synonymous_variant 0.12
gyrA 7683 c.382A>C synonymous_variant 0.11
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 1.0
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoC 764611 c.1242G>C synonymous_variant 0.14
rpoC 764626 c.1257C>T synonymous_variant 0.14
rpoC 764632 c.1263T>C synonymous_variant 0.15
rpoC 764650 c.1281G>T synonymous_variant 0.15
rpoC 764656 c.1287C>G synonymous_variant 0.14
rpoC 764668 c.1299C>T synonymous_variant 0.12
rpoC 764752 c.1383G>C synonymous_variant 0.11
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 766978 c.3609C>A synonymous_variant 0.33
rpoC 766996 c.3627C>T synonymous_variant 0.29
rpoC 767033 c.3664_3666delTCGinsAGT synonymous_variant 0.29
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776383 c.2097delC frameshift_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406195 c.1146G>A synonymous_variant 0.11
embR 1416432 p.Ala306Thr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475907 n.2253delA non_coding_transcript_exon_variant 0.17
rpsA 1833924 p.Gly128Asp missense_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168981 c.1632A>G synonymous_variant 0.17
PPE35 2169253 p.Ala454Thr missense_variant 0.15
PPE35 2169783 p.Thr277Lys missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290179 c.-938G>T upstream_gene_variant 0.2
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
ribD 2987231 c.393G>T synonymous_variant 0.14
Rv2752c 3065553 c.639A>G synonymous_variant 0.15
Rv2752c 3065562 c.630T>C synonymous_variant 0.15
Rv2752c 3065569 p.Ile208His missense_variant 0.15
Rv2752c 3065576 p.Ala206Ser missense_variant 0.15
Rv2752c 3065577 c.615C>T synonymous_variant 0.15
Rv2752c 3065580 c.612G>C synonymous_variant 0.15
Rv2752c 3065583 c.609G>A synonymous_variant 0.14
Rv2752c 3065594 c.598C>T synonymous_variant 0.12
Rv2752c 3065595 p.Leu199Phe missense_variant 0.12
Rv2752c 3065607 c.585C>G synonymous_variant 0.12
Rv2752c 3065612 p.Thr194Ala missense_variant 0.12
Rv2752c 3066040 p.Gly51Thr missense_variant 0.17
Rv2752c 3066042 c.150T>C synonymous_variant 0.17
Rv2752c 3066050 p.Leu48Met missense_variant 0.17
Rv2752c 3066054 c.138T>C synonymous_variant 0.17
Rv2752c 3066066 c.126T>C synonymous_variant 0.13
Rv2752c 3066071 c.121T>C synonymous_variant 0.13
Rv2752c 3066075 c.117A>G synonymous_variant 0.13
Rv2752c 3066087 c.105A>G synonymous_variant 0.13
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449135 p.Gln211Arg missense_variant 0.25
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
rpoA 3878205 c.303T>C synonymous_variant 0.14
rpoA 3878217 c.291A>G synonymous_variant 0.14
rpoA 3878247 c.261G>C synonymous_variant 0.16
rpoA 3878276 c.232C>T synonymous_variant 0.15
rpoA 3878415 c.93C>T synonymous_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embB 4248220 c.1707A>G synonymous_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0