TB-Profiler result

Run: ERR4830826
Summary

Run ID: ERR4830826

Sample name:

Date: 20-10-2023 06:46:18

Number of reads: 2360963

Percentage reads mapped: 99.69

Strain: lineage4.8;lineage4.2.2.2

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 p.Ser315Thr (0.13)
Ethambutol R embB p.Met306Ile (0.15), embB p.Gly406Asp (0.14)
Pyrazinamide R pncA p.Phe58Leu (0.17)
Streptomycin R gid p.Gly69Asp (0.12)
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
lineage4.2 Euro-American H;T;LAM None 0.12
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 0.82
lineage4.2.2 Euro-American (Ural) T;LAM7-TUR None 0.13
lineage4.2.2.2 Euro-American (Ural) T;LAM7-TUR None 0.13
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 2155168 p.Ser315Thr missense_variant 0.13 isoniazid
pncA 2289068 p.Phe58Leu missense_variant 0.17 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 0.15 ethambutol
embB 4247730 p.Gly406Asp missense_variant 0.14 ethambutol
gid 4407997 p.Gly69Asp missense_variant 0.12 streptomycin
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 8688 p.Ala463Ser missense_variant 0.18
gyrA 9304 p.Gly668Asp missense_variant 0.13
mshA 576077 c.730C>T synonymous_variant 0.15
rpoB 760975 p.Met390Thr missense_variant 0.85
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
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.85
rrl 1475090 n.1433A>C non_coding_transcript_exon_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168149 p.Pro822Ser missense_variant 0.77
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726146 c.-47_-46insT upstream_gene_variant 0.23
thyA 3074100 p.Asp124Glu missense_variant 0.89
ald 3086742 c.-78A>C upstream_gene_variant 0.17
ald 3086767 c.-53A>C upstream_gene_variant 0.81
ald 3086788 c.-32T>C upstream_gene_variant 0.22
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
aftB 4267715 c.1122G>A synonymous_variant 0.92
ethA 4327472 c.2T>G start_lost 0.21
whiB6 4338595 c.-75delG upstream_gene_variant 1.0