TB-Profiler result

Run: ERR4799718
Summary

Run ID: ERR4799718

Sample name:

Date: 20-10-2023 04:02:20

Number of reads: 3303652

Percentage reads mapped: 99.5

Strain: lineage4.1.1.3

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 (0.99), katG p.Ser315Thr (0.99)
Ethambutol R embB p.Met306Ile (0.97), embB p.Gln497Arg (0.95)
Pyrazinamide
Streptomycin
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
Cycloserine
Ethionamide R fabG1 c.-15C>T (0.99)
Clofazimine
Para-aminosalicylic_acid R thyA c.-2233_*1762del (0.97)
Delamanid
Bedaquiline
Linezolid
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.1 Euro-American T;X;H None 0.98
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 0.98
lineage4.1.1.3 Euro-American (X-type) X1;X3 RD193 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
fabG1 1673425 c.-15C>T upstream_gene_variant 0.99 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 0.99 isoniazid
embB 4247431 p.Met306Ile missense_variant 0.97 ethambutol
embB 4248003 p.Gln497Arg missense_variant 0.95 ethambutol
thyA 3071917 c.-2233_*1762del transcript_ablation 0.97 para-aminosalicylic_acid
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
rpoB 759694 c.-113C>T upstream_gene_variant 0.99
rpoC 764817 p.Val483Gly missense_variant 0.99
rpoC 765150 p.Gly594Glu missense_variant 0.96
mmpL5 775639 p.Ile948Val missense_variant 1.0
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
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
thyX 3067949 c.-4C>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
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embB 4249408 c.2895G>A synonymous_variant 0.99
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407976 p.Gly76Asp missense_variant 0.98
pncA 2288650 c.523_*30delNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNC stop_lost&conservative_inframe_deletion&splice_region_variant 0.96