TB-Profiler result

Run: ERR4813072
Summary

Run ID: ERR4813072

Sample name:

Date: 01-04-2023 12:31:18

Number of reads: 682123

Percentage reads mapped: 99.53

Strain: lineage4.3.3

Drug-resistance: MDR-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
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.3 Euro-American (LAM) LAM;T RD115 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
rpoB 761110 p.Asp435Val missense_variant 1.0 rifampicin
tlyA 1918634 p.Gly232Asp missense_variant 1.0 capreomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289213 p.Gln10Arg missense_variant 1.0 pyrazinamide
embB 4247469 p.Tyr319Ser missense_variant 1.0 ethambutol
gid 4407952 p.Pro84Leu missense_variant 1.0 streptomycin
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 5366 p.His43Tyr missense_variant 0.11
gyrB 6477 p.Ser413Leu missense_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8040 p.Gly247Ser missense_variant 1.0
gyrA 8969 c.1668G>T synonymous_variant 0.11
gyrA 9304 p.Gly668Asp missense_variant 1.0
ccsA 619833 c.-58T>C upstream_gene_variant 0.25
rpoB 759647 c.-160T>C upstream_gene_variant 0.12
rpoB 761814 p.Ala670Thr missense_variant 0.11
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 765450 p.Ala694Val missense_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801280 p.Ala158Ser missense_variant 0.12
embR 1417532 c.-185T>C upstream_gene_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673288 c.-152G>T upstream_gene_variant 0.11
fabG1 1673638 p.Ala67Ser missense_variant 0.14
inhA 1673658 c.-544G>A upstream_gene_variant 0.14
inhA 1674550 p.Ser117Pro missense_variant 0.2
rpsA 1834985 c.1445dupG frameshift_variant&stop_lost&splice_region_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918361 p.Pro141Gln missense_variant 0.12
ndh 2102776 c.267C>G synonymous_variant 0.12
PPE35 2167684 p.Leu977Met missense_variant 0.11
PPE35 2168998 p.Ile539Val missense_variant 1.0
PPE35 2169973 p.Gly214Cys missense_variant 0.12
PPE35 2170629 c.-17C>A upstream_gene_variant 0.11
Rv1979c 2222240 p.Leu309Met missense_variant 0.29
Rv1979c 2222268 c.897C>A synonymous_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289412 c.-171C>A upstream_gene_variant 0.12
kasA 2518443 p.Val110Ala missense_variant 0.12
kasA 2518919 p.Gly269Ser missense_variant 1.0
kasA 2519291 p.Asp393Asn missense_variant 0.17
eis 2714545 p.Glu263Gly missense_variant 0.14
folC 2747518 c.81G>T synonymous_variant 0.2
ribD 2987487 p.Pro217Thr missense_variant 0.11
ribD 2987498 c.660C>A synonymous_variant 0.13
thyX 3067611 p.Lys112Arg missense_variant 0.11
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339653 c.537delA frameshift_variant 0.2
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.96
Rv3236c 3612967 c.150G>A synonymous_variant 0.18
fbiB 3642807 p.Ala425Thr missense_variant 0.12
ddn 3986798 c.-46G>T upstream_gene_variant 0.11
ddn 3986801 c.-43G>T upstream_gene_variant 0.11
ddn 3987022 p.Arg60Gln missense_variant 0.15
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4038397 p.Ala770Thr missense_variant 0.11
embC 4240518 p.Asp219Val missense_variant 0.15
embC 4242182 p.Ala774Ser missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245907 p.Leu892Pro missense_variant 0.4
aftB 4269003 c.-167C>A upstream_gene_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407740 p.Pro155Thr missense_variant 0.25
gid 4407934 p.Leu90His missense_variant 0.2
gid 4408156 p.Leu16Arg missense_variant 1.0