TB-Profiler result

Run: SRR5341398
Summary

Run ID: SRR5341398

Sample name:

Date: 20-10-2023 18:52:54

Number of reads: 1715335

Percentage reads mapped: 99.51

Strain: lineage4.1.1.3;lineage3

Drug-resistance: Pre-XDR-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.Ser450Leu (1.00)
Isoniazid R fabG1 c.-15C>T (0.50), katG p.Ser315Thr (1.00)
Ethambutol R embB p.Met306Ile (0.64), embB p.Tyr319Ser (0.33)
Pyrazinamide R pncA c.382dupG (0.61)
Streptomycin R gid p.Gln125* (0.33)
Fluoroquinolones R gyrA p.Ala90Val (0.62)
Moxifloxacin R gyrA p.Ala90Val (0.62)
Ofloxacin R gyrA p.Ala90Val (0.62)
Levofloxacin R gyrA p.Ala90Val (0.62)
Ciprofloxacin R gyrA p.Ala90Val (0.62)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R fabG1 c.-15C>T (0.50)
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 0.63
lineage4 Euro-American LAM;T;S;X;H None 0.31
lineage4.1 Euro-American T;X;H None 0.36
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 0.37
lineage4.1.1.3 Euro-American (X-type) X1;X3 RD193 0.33
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
gyrA 7570 p.Ala90Val missense_variant 0.62 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.5 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288859 c.382dupG frameshift_variant 0.61 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 0.64 ethambutol
embB 4247469 p.Tyr319Ser missense_variant 0.33 ethambutol
gid 4407830 p.Gln125* stop_gained 0.33 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 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.55
rpoB 759746 c.-61C>T upstream_gene_variant 0.6
rpoB 761993 c.2187C>T synonymous_variant 0.7
rpoC 762434 c.-936T>G upstream_gene_variant 0.57
rpoC 763031 c.-339T>C upstream_gene_variant 0.84
rpoC 764819 p.Trp484Gly missense_variant 0.67
rpoC 765150 p.Gly594Glu missense_variant 0.39
rpoC 766196 p.Asp943Asn missense_variant 0.34
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.7
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2153915 p.Asn733Asp missense_variant 0.42
katG 2154724 p.Arg463Leu missense_variant 0.75
PPE35 2167926 p.Leu896Ser missense_variant 0.57
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.58
pncA 2289365 c.-125delC upstream_gene_variant 0.73
ahpC 2726105 c.-88G>A upstream_gene_variant 0.61
folC 2747466 c.130_132dupGAT conservative_inframe_insertion 0.76
Rv2752c 3064991 p.Arg401Gly missense_variant 0.55
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
alr 3841473 c.-53G>A upstream_gene_variant 0.69
embC 4242075 p.Arg738Gln missense_variant 0.66
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.41
embB 4249408 c.2895G>A synonymous_variant 0.33
ubiA 4269320 p.Leu172Val missense_variant 0.39
ethR 4327691 p.Asp48Gly missense_variant 0.43
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.63
gid 4408123 c.79delG frameshift_variant 0.56