TB-Profiler result

Run: ERR4797114
Summary

Run ID: ERR4797114

Sample name:

Date: 20-10-2023 02:11:19

Number of reads: 2005015

Percentage reads mapped: 99.55

Strain: lineage4.3.3;lineage3

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
Rifampicin R rpoB p.Leu452Pro (0.29)
Isoniazid R fabG1 c.-15C>T (0.13), katG p.Ser315Thr (0.24)
Ethambutol
Pyrazinamide R pncA p.His71Tyr (0.25)
Streptomycin R gid c.102delG (0.83)
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R fabG1 c.-15C>T (0.13)
Clofazimine
Para-aminosalicylic_acid
Delamanid
Bedaquiline
Linezolid
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage3 East-African-Indian CAS RD750 0.77
lineage4 Euro-American LAM;T;S;X;H None 0.27
lineage4.3 Euro-American (LAM) mainly-LAM None 0.18
lineage4.3.3 Euro-American (LAM) LAM;T RD115 0.27
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 761161 p.Leu452Pro missense_variant 0.29 rifampicin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.13 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 0.24 isoniazid
pncA 2289031 p.His71Tyr missense_variant 0.25 pyrazinamide
gid 4408100 c.102delG frameshift_variant 0.83 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8040 p.Gly247Ser missense_variant 0.13
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.8
rpoB 759746 c.-61C>T upstream_gene_variant 0.67
rpoC 762434 c.-936T>G upstream_gene_variant 0.81
rpoC 763031 c.-339T>C upstream_gene_variant 0.8
rpoC 764995 c.1626C>G synonymous_variant 0.25
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.75
mmpL5 778780 c.-300G>A upstream_gene_variant 0.78
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1407363 c.-23C>T upstream_gene_variant 0.3
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 0.83
katG 2156196 c.-85C>T upstream_gene_variant 0.24
PPE35 2167926 p.Leu896Ser missense_variant 0.8
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.79
pncA 2289365 c.-125delC upstream_gene_variant 0.7
kasA 2518919 p.Gly269Ser missense_variant 0.28
ahpC 2726105 c.-88G>A upstream_gene_variant 0.76
folC 2746340 p.Ala420Val missense_variant 0.34
thyA 3073868 p.Thr202Ala missense_variant 0.27
thyA 3074096 p.Arg126Gly missense_variant 0.21
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 0.13
embC 4242075 p.Arg738Gln missense_variant 0.67
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243210 c.-23C>T upstream_gene_variant 0.71
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.68
gid 4408156 p.Leu16Arg missense_variant 0.12