TB-Profiler result

Run: ERR5866119

Summary

Run ID: ERR5866119

Sample name:

Date: 02-04-2023 00:30:58

Number of reads: 777410

Percentage reads mapped: 99.27

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 761100 p.Gln432Lys missense_variant 1.0 rifampicin
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 8040 p.Gly247Ser missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9410 p.Met703Ile missense_variant 0.11
rpoB 762201 p.Lys799Gln missense_variant 1.0
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpR5 779363 p.Leu125Gln missense_variant 0.15
mmpR5 779486 c.497G>T stop_lost&splice_region_variant 0.18
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781739 p.Gln60His missense_variant 0.11
Rv1258c 1406943 c.397_398insGC frameshift_variant 0.12
Rv1258c 1406946 p.Ala132Gly missense_variant 0.11
Rv1258c 1406948 c.391_392delGC frameshift_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1833694 c.153G>C synonymous_variant 0.1
rpsA 1834073 p.Lys178* stop_gained 0.11
rpsA 1834268 p.Lys243Glu missense_variant 0.17
rpsA 1834836 p.Met432Thr missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2156196 c.-85C>T upstream_gene_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.32
PPE35 2170053 p.Thr187Ser missense_variant 0.33
PPE35 2170342 c.250_270delGAGCAGGCGGCCACCCAGGCC conservative_inframe_deletion 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 1.0
kasA 2519240 p.Pro376Ser missense_variant 0.12
folC 2746340 p.Ala420Val missense_variant 1.0
ribD 2987267 c.429C>T synonymous_variant 0.13
Rv2752c 3066060 p.Asp44Glu missense_variant 0.11
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4038968 c.1737G>A synonymous_variant 1.0
panD 4043992 p.Arg97Leu missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244969 c.1737G>T synonymous_variant 0.12
embA 4246122 p.Leu964Met missense_variant 0.15
embB 4246548 p.Pro12Gln missense_variant 0.18
embB 4246555 c.42G>C synonymous_variant 0.17
embB 4246556 p.Ala15Pro missense_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407808 p.Asp132Gly missense_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0