TB-Profiler result

Run: ERR1035291
Summary

Run ID: ERR1035291

Sample name:

Date: 20-10-2023 21:38:08

Number of reads: 5809192

Percentage reads mapped: 99.81

Strain: lineage4.3.4.2

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 c.1306_1311delCAGAAC (1.00)
Isoniazid R ahpC c.-74G>A (1.00)
Ethambutol R embB p.Gln497Arg (1.00)
Pyrazinamide R pncA p.Cys72Arg (0.87)
Streptomycin
Fluoroquinolones R gyrA p.Ser91Pro (0.90)
Moxifloxacin R gyrA p.Ser91Pro (0.90)
Ofloxacin R gyrA p.Ser91Pro (0.90)
Levofloxacin R gyrA p.Ser91Pro (0.90)
Ciprofloxacin R gyrA p.Ser91Pro (0.90)
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 1.0
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.4 Euro-American (LAM) LAM RD174 1.0
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 1.0
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 7572 p.Ser91Pro missense_variant 0.9 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761109 c.1306_1311delCAGAAC conservative_inframe_deletion 1.0 rifampicin
pncA 2289028 p.Cys72Arg missense_variant 0.87 pyrazinamide
ahpC 2726119 c.-74G>A upstream_gene_variant 1.0 isoniazid
embB 4248003 p.Gln497Arg missense_variant 1.0 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
gyrB 6140 p.Val301Leu missense_variant 1.0
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 764995 c.1626C>G synonymous_variant 1.0
rpoC 766838 p.Ile1157Val missense_variant 0.99
rpoC 767058 p.Thr1230Ile missense_variant 0.97
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 0.98
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473965 n.308G>T non_coding_transcript_exon_variant 1.0
rpsA 1833469 c.-73G>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 0.99
katG 2154932 p.Thr394Pro missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 0.99
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
alr 3840719 c.702A>G synonymous_variant 0.99
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244531 c.1299G>A synonymous_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 0.99