TB-Profiler result

Run: ERR5866120
Summary

Run ID: ERR5866120

Sample name:

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

Number of reads: 835971

Percentage reads mapped: 99.22

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 0.99
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
katG 2155030 p.Ala361Asp missense_variant 0.13 isoniazid
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
rpoB 762201 p.Lys799Gln missense_variant 1.0
rpoC 763947 p.Ala193Val missense_variant 0.11
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 765726 p.Gly786Val missense_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775734 p.Phe916Ser missense_variant 0.12
mmpL5 776587 p.Pro632Ser missense_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406446 p.Gly299Ser missense_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1674128 p.Ser230Asn missense_variant 0.17
inhA 1674633 c.432C>A synonymous_variant 0.14
rpsA 1833878 c.341delG frameshift_variant 0.14
rpsA 1834836 p.Met432Thr missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155717 p.Leu132Pro missense_variant 0.18
katG 2156196 c.-85C>T upstream_gene_variant 1.0
PPE35 2168389 p.Gln742Lys missense_variant 0.12
PPE35 2170048 p.Leu189Val missense_variant 0.25
PPE35 2170053 p.Thr187Ser missense_variant 0.24
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
folC 2746340 p.Ala420Val missense_variant 1.0
Rv2752c 3066030 c.162G>A synonymous_variant 0.11
Rv2752c 3067126 c.-935C>A upstream_gene_variant 0.12
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087895 c.1081delG frameshift_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiA 3641321 p.Leu260Pro missense_variant 0.12
rpoA 3877481 p.Glu343* stop_gained 0.12
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4038968 c.1737G>A synonymous_variant 1.0
clpC1 4039841 p.Glu288Asp missense_variant 0.13
embC 4240918 c.1056G>T synonymous_variant 0.11
embC 4242491 c.2632_2638delGACAGGG frameshift_variant 0.14
embC 4242502 c.2642_2643insCTGTCCC frameshift_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246214 c.-300C>T upstream_gene_variant 0.11
embB 4248317 p.Val602Pro missense_variant 0.1
embB 4248321 p.Gly603Ala missense_variant 0.1
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407808 p.Asp132Gly missense_variant 1.0
gid 4408071 c.132A>T synonymous_variant 0.12
gid 4408156 p.Leu16Arg missense_variant 1.0