TB-Profiler result

Run: ERR4553782
Summary

Run ID: ERR4553782

Sample name:

Date: 01-04-2023 06:20:31

Number of reads: 1987446

Percentage reads mapped: 99.54

Strain: lineage1.1.3

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
lineage1 Indo-Oceanic EAI RD239 0.11
lineage1.1.3 Indo-Oceanic EAI6 RD239 0.97
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 761155 p.Ser450Leu missense_variant 1.0 rifampicin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.33 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288998 p.His82Asp missense_variant 0.27 pyrazinamide
pncA 2289142 p.Tyr34Asp missense_variant 0.41 pyrazinamide
embB 4247553 p.Ser347Thr missense_variant 0.49 ethambutol
embB 4248003 p.Gln497Arg missense_variant 0.16 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 0.97
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 0.96
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.35
mshA 576675 p.Arg443His missense_variant 1.0
rpoB 759886 p.Pro27His missense_variant 1.0
rpoB 761005 p.Thr400Asn missense_variant 0.95
rpoC 763031 c.-339T>C upstream_gene_variant 0.98
rpoC 763884 p.Ala172Val missense_variant 0.75
rpoC 763886 c.517C>A synonymous_variant 0.75
rpoC 765230 p.Ala621Thr missense_variant 0.88
rpoC 766042 c.2673C>T synonymous_variant 0.96
rpoC 767308 c.3939C>T synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.99
mmpL5 778099 p.Asp128Asn missense_variant 0.98
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1407190 c.123_150delTGGGCAGGCCTCGATCGTGGCCAGTGCG frameshift_variant 1.0
embR 1416574 c.774A>G synonymous_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 0.95
Rv1979c 2222308 p.Asp286Gly missense_variant 0.93
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 0.97
ahpC 2726590 p.Arg133His missense_variant 0.98
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
ald 3086767 c.-53A>T upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.99
fprA 3474597 c.591C>A synonymous_variant 0.75
fprA 3475159 p.Asn385Asp missense_variant 1.0
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 0.6
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4243056 p.Pro1065Leu missense_variant 1.0
embA 4243848 p.Val206Met missense_variant 0.98
embA 4245314 c.2082G>C synonymous_variant 0.99
embA 4245969 p.Pro913Ser missense_variant 0.5
embB 4246529 p.Ser6Arg missense_variant 0.22
embB 4247646 p.Glu378Ala missense_variant 0.67
ubiA 4269133 p.Gly234Val missense_variant 0.95
ubiA 4269387 p.Glu149Asp missense_variant 0.86
aftB 4269606 c.-770T>C upstream_gene_variant 0.82
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407780 c.423G>A synonymous_variant 0.92
gid 4407873 c.330G>T synonymous_variant 0.8
gid 4408252 c.-50A>G upstream_gene_variant 1.0
gid 4408338 c.-136A>G upstream_gene_variant 1.0
Rv1258c 1407190 c.122_150delNNNNNNNNNNNNNNNNNNNNNNNNNNNNA frameshift_variant 1.0