TB-Profiler result

Run: ERR4799165

Summary

Run ID: ERR4799165

Sample name:

Date: 20-10-2023 03:30:22

Number of reads: 2457489

Percentage reads mapped: 99.49

Strain: 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), rpoC p.Ile491Thr (0.97)
Isoniazid R fabG1 c.-15C>T (0.97), inhA p.Ser94Ala (0.96), katG p.Thr380Ile (1.00)
Ethambutol R embB p.Met306Val (0.99)
Pyrazinamide
Streptomycin R rpsL p.Lys88Met (1.00)
Fluoroquinolones R gyrA p.Asp94Asn (0.98)
Moxifloxacin R gyrA p.Asp94Asn (0.98)
Ofloxacin R gyrA p.Asp94Asn (0.98)
Levofloxacin R gyrA p.Asp94Asn (0.98)
Ciprofloxacin R gyrA p.Asp94Asn (0.98)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin R eis c.-10G>C (0.93), eis c.-10G>C (0.93)
Cycloserine
Ethionamide R fabG1 c.-15C>T (0.97), inhA p.Ser94Ala (0.96)
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
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 7581 p.Asp94Asn missense_variant 0.98 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpoC 764841 p.Ile491Thr missense_variant 0.97 rifampicin
rpsL 781822 p.Lys88Met missense_variant 1.0 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.97 isoniazid, ethionamide
inhA 1674481 p.Ser94Ala missense_variant 0.96 isoniazid, ethionamide
katG 2154973 p.Thr380Ile missense_variant 1.0 isoniazid
eis 2715342 c.-10G>C upstream_gene_variant 0.93 kanamycin, kanamycin
embB 4247429 p.Met306Val missense_variant 0.99 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 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 0.99
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpR5 779215 p.Gln76Lys missense_variant 0.94
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800726 c.-83G>T upstream_gene_variant 0.94
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 0.98
katG 2155880 p.Arg78Trp missense_variant 0.95
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288852 c.387_389delTGT disruptive_inframe_deletion 1.0
pncA 2289047 c.195C>T synonymous_variant 0.95
pncA 2289365 c.-125delC upstream_gene_variant 1.0
eis 2715189 c.144C>T synonymous_variant 0.99
ahpC 2726105 c.-88G>A upstream_gene_variant 0.97
ahpC 2726181 c.-12_-11insT upstream_gene_variant 0.94
Rv2752c 3065589 p.Cys201* stop_gained 1.0
thyA 3074495 c.-24C>T upstream_gene_variant 0.99
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
alr 3841362 p.Thr20Met missense_variant 0.95
alr 3841511 c.-91C>T upstream_gene_variant 0.97
embC 4242075 p.Arg738Gln missense_variant 0.98
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0