TB-Profiler result

Run: ERR1213928

Summary

Run ID: ERR1213928

Sample name:

Date: 19-10-2023 20:55:13

Number of reads: 4280424

Percentage reads mapped: 98.59

Strain: lineage4.3.3

Drug-resistance: MDR-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.Asp435Val (0.93)
Isoniazid R katG p.Ser315Thr (1.00)
Ethambutol R embB p.Tyr319Ser (0.96)
Pyrazinamide R pncA p.Gln10Arg (1.00)
Streptomycin R gid p.Pro84Leu (1.00)
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
lineage4.3 Euro-American (LAM) mainly-LAM None 0.98
lineage4.3.3 Euro-American (LAM) LAM;T RD115 0.97
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
rpoB 761110 p.Asp435Val missense_variant 0.93 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289213 p.Gln10Arg missense_variant 1.0 pyrazinamide
embB 4247469 p.Tyr319Ser missense_variant 0.96 ethambutol
gid 4407952 p.Pro84Leu missense_variant 1.0 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 7585 p.Ser95Thr missense_variant 1.0
gyrA 8040 p.Gly247Ser missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoC 764995 c.1626C>G synonymous_variant 1.0
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 1473752 n.95G>T non_coding_transcript_exon_variant 0.45
rrl 1473806 n.149C>T non_coding_transcript_exon_variant 0.52
rrl 1473815 n.158T>C non_coding_transcript_exon_variant 0.53
rrl 1473836 n.179A>G non_coding_transcript_exon_variant 0.5
rrl 1473876 n.219G>A non_coding_transcript_exon_variant 0.26
rrl 1473877 n.220G>A non_coding_transcript_exon_variant 0.26
rrl 1474028 n.371T>C non_coding_transcript_exon_variant 0.17
rrl 1474029 n.372G>A non_coding_transcript_exon_variant 0.18
rrl 1474034 n.377G>A non_coding_transcript_exon_variant 0.17
rrl 1474040 n.383G>A non_coding_transcript_exon_variant 0.18
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.22
rrl 1476597 n.2940G>A non_coding_transcript_exon_variant 0.28
rrl 1476628 n.2971T>A non_coding_transcript_exon_variant 0.32
rpsA 1834985 c.1445dupG frameshift_variant&stop_lost&splice_region_variant 0.88
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168998 p.Ile539Val missense_variant 0.98
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 0.96
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embC 4242182 p.Ala774Ser missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0