TB-Profiler result

Run: ERR133938

Summary

Run ID: ERR133938

Sample name:

Date: 21-10-2023 03:43:11

Number of reads: 8938516

Percentage reads mapped: 99.66

Strain: lineage4.8;lineage4.1

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.Ser450Leu (0.20)
Isoniazid R katG p.Ser315Thr (0.13)
Ethambutol
Pyrazinamide
Streptomycin R rpsL p.Lys43Arg (0.14)
Fluoroquinolones R gyrA p.Ala90Val (0.15)
Moxifloxacin R gyrA p.Ala90Val (0.15)
Ofloxacin R gyrA p.Ala90Val (0.15)
Levofloxacin R gyrA p.Ala90Val (0.15)
Ciprofloxacin R gyrA p.Ala90Val (0.15)
Aminoglycosides
Amikacin R eis c.-14C>T (0.17)
Capreomycin
Kanamycin R eis c.-14C>T (0.17)
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 1.0
lineage4.1 Euro-American T;X;H None 0.15
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 0.85
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 0.15 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.2 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.14 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.13 isoniazid
eis 2715346 c.-14C>T upstream_gene_variant 0.17 kanamycin, amikacin
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 0.17
gyrA 9304 p.Gly668Asp missense_variant 0.18
rpoC 764438 c.1069C>T synonymous_variant 0.14
rpoC 765150 p.Gly594Glu missense_variant 0.15
rpoC 765863 p.Ile832Val missense_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801019 p.Thr71Ala missense_variant 0.18
atpE 1461209 c.165C>T synonymous_variant 0.19
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.84
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168149 p.Pro822Ser missense_variant 0.86
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 0.19
Rv3083 3448497 c.-7T>A upstream_gene_variant 0.25
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.18
clpC1 4039729 p.Asp326Asn missense_variant 0.84
embC 4242584 p.Ala908Thr missense_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.11
embB 4247296 c.783G>A synonymous_variant 0.17
embB 4249408 c.2895G>A synonymous_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0