TB-Profiler result

Run: SRR2100350
Summary

Run ID: SRR2100350

Sample name:

Date: 19-10-2023 15:50:24

Number of reads: 4169506

Percentage reads mapped: 99.35

Strain: lineage3.1.3

Drug-resistance: HR-TB

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin
Isoniazid R fabG1 c.-15C>T (0.95), katG p.Ser315Thr (0.96)
Ethambutol
Pyrazinamide
Streptomycin R gid c.102delG (0.98)
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R fabG1 c.-15C>T (0.95)
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 0.98
lineage3.1.3 East-African-Indian CAS RD750 0.99
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
fabG1 1673425 c.-15C>T upstream_gene_variant 0.95 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 0.96 isoniazid
gid 4408100 c.102delG frameshift_variant 0.98 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 1.0
rpoC 762434 c.-936T>G upstream_gene_variant 0.96
rpoC 763031 c.-339T>C upstream_gene_variant 0.96
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834159 c.618G>A synonymous_variant 0.99
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918474 p.Pro179Ser missense_variant 0.96
katG 2154724 p.Arg463Leu missense_variant 0.99
katG 2154833 p.Leu427Phe missense_variant 0.94
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2222732 c.432delT frameshift_variant 0.95
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 0.99
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
folC 2747132 p.Thr156Ile missense_variant 0.96
Rv2752c 3065181 c.1010_1011insA frameshift_variant 0.99
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
embC 4242075 p.Arg738Gln missense_variant 0.97
embA 4242643 c.-590C>T upstream_gene_variant 0.97
embB 4249195 c.2682C>A synonymous_variant 0.97
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.95
gid 4408175 p.Ala10Pro missense_variant 0.98