TB-Profiler result

Run: ERR1035327
Summary

Run ID: ERR1035327

Sample name:

Date: 20-10-2023 21:39:35

Number of reads: 6194748

Percentage reads mapped: 94.11

Strain: lineage4.7

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.Asp435Phe (1.00)
Isoniazid R katG p.Ser315Thr (1.00)
Ethambutol R embB p.Met306Ile (1.00)
Pyrazinamide R pncA c.-11A>G (1.00)
Streptomycin R rrs n.888G>A (0.19)
Fluoroquinolones R gyrA p.Asp94Asn (1.00)
Moxifloxacin R gyrA p.Asp94Asn (1.00)
Ofloxacin R gyrA p.Asp94Asn (1.00)
Levofloxacin R gyrA p.Asp94Asn (1.00)
Ciprofloxacin R gyrA p.Asp94Asn (1.00)
Aminoglycosides R rrs n.1401A>G (0.91)
Amikacin R rrs n.1401A>G (0.91)
Capreomycin R rrs n.1401A>G (0.91)
Kanamycin R rrs n.1401A>G (0.91)
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
lineage4.7 Euro-American (mainly T) T1;T5 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
gyrA 7581 p.Asp94Asn missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761109 p.Asp435Phe missense_variant 1.0 rifampicin
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.19 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.91 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289252 c.-11A>G upstream_gene_variant 1.0 pyrazinamide
embB 4247431 p.Met306Ile 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
gyrA 7362 p.Glu21Gln missense_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
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.13
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.13
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.12
rrs 1472583 n.738T>C non_coding_transcript_exon_variant 0.12
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.13
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.13
rrs 1472607 n.762G>A non_coding_transcript_exon_variant 0.13
rrs 1472612 n.767G>T non_coding_transcript_exon_variant 0.13
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.19
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.19
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.2
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.18
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.16
rrl 1474294 n.637C>G non_coding_transcript_exon_variant 1.0
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.15
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.16
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.19
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.18
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.19
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.2
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.22
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.22
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.22
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ald 3087009 c.191dupT frameshift_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4249732 c.3219C>G synonymous_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0