TB-Profiler result

Run: ERR502938
Summary

Run ID: ERR502938

Sample name:

Date: 19-10-2023 12:44:23

Number of reads: 2697242

Percentage reads mapped: 99.52

Strain: lineage4.4.2

Drug-resistance: HR-TB

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin
Isoniazid R katG c.-7G>A (0.31)
Ethambutol
Pyrazinamide
Streptomycin
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
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
lineage4.4 Euro-American S;T None 0.99
lineage4.4.2 Euro-American T1;T2 None 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
katG 2156118 c.-7G>A upstream_gene_variant 0.31 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
ccsA 620609 p.Phe240Tyr missense_variant 1.0
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 1475408 n.1751C>T non_coding_transcript_exon_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154203 p.Asn637Asp missense_variant 0.24
katG 2155351 p.Arg254His missense_variant 0.31
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv2752c 3066099 p.Met31Ile missense_variant 1.0
thyX 3068049 c.-104C>A upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448727 p.Leu75Arg missense_variant 1.0
Rv3083 3449032 c.531_544delCAAGAAGGTCGTCG frameshift_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243991 c.759T>G synonymous_variant 0.97
embB 4246508 c.-6G>A upstream_gene_variant 0.96
aftB 4268928 c.-92C>T upstream_gene_variant 1.0
aftB 4269375 c.-539G>A upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0