TB-Profiler result

Run: SRR25827496
Summary

Run ID: SRR25827496

Sample name:

Date: 15-03-2024 17:31:52

Number of reads: 5527692

Percentage reads mapped: 97.85

Strain: lineage4.1.1.1

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.Ser428Ile (0.82), rpoB p.Leu430Pro (1.00)
Isoniazid R katG p.Ser315Thr (0.88)
Ethambutol
Pyrazinamide
Streptomycin
Fluoroquinolones R gyrA p.Asp94Asn (0.92)
Moxifloxacin R gyrA p.Asp94Asn (0.92)
Ofloxacin R gyrA p.Asp94Asn (0.92)
Levofloxacin R gyrA p.Asp94Asn (0.92)
Ciprofloxacin R gyrA p.Asp94Asn (0.92)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide
Clofazimine
Para-aminosalicylic_acid
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 0.93
lineage4.1 Euro-American T;X;H None 0.87
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 0.88
lineage4.1.1.1 Euro-American (X-type) X2 RD183 0.87
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 0.92 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761089 p.Ser428Ile missense_variant 0.82 rifampicin
rpoB 761095 p.Leu430Pro missense_variant 1.0 rifampicin
katG 2155167 p.Ser315Thr missense_variant 0.88 isoniazid
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
rpoC 765150 p.Gly594Glu missense_variant 0.88
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
rrs 1473371 n.1526C>T non_coding_transcript_exon_variant 0.8
inhA 1673368 c.-834A>G upstream_gene_variant 0.86
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726210 c.18T>C synonymous_variant 0.88
ribD 2987506 p.Leu223Arg missense_variant 0.17
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiA 3641447 p.Thr302Met missense_variant 0.86
rpoA 3877553 p.Glu319Lys missense_variant 0.88
embC 4240897 c.1035C>G synonymous_variant 0.93
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.86
embA 4245835 p.Leu868Arg missense_variant 0.22
embB 4247507 p.Trp332Arg missense_variant 0.86
embB 4249408 c.2895G>A synonymous_variant 0.9
whiB6 4338595 c.-75delG upstream_gene_variant 1.0