TB-Profiler result

Run: ERR2513859

Summary

Run ID: ERR2513859

Sample name:

Date: 20-10-2023 11:18:24

Number of reads: 4182330

Percentage reads mapped: 99.57

Strain: lineage4.8.2;lineage4.1.1.3.1

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.Ile491Phe (0.79)
Isoniazid
Ethambutol R embB p.Met306Ile (0.85)
Pyrazinamide
Streptomycin R gid c.102delG (0.90)
Fluoroquinolones R gyrA p.Asp94Gly (0.86)
Moxifloxacin R gyrA p.Asp94Gly (0.86)
Ofloxacin R gyrA p.Asp94Gly (0.86)
Levofloxacin R gyrA p.Asp94Gly (0.86)
Ciprofloxacin R gyrA p.Asp94Gly (0.86)
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
lineage4.1 Euro-American T;X;H None 0.88
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 0.1
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 0.88
lineage4.8.2 Euro-American (mainly T) T1;T2;T3;T5 RD219 0.08
lineage4.1.1.3 Euro-American (X-type) X1;X3 RD193 0.89
lineage4.1.1.3.1 Euro-American (X-type) X1;X3 RD193 0.87
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 7582 p.Asp94Gly missense_variant 0.86 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761277 p.Ile491Phe missense_variant 0.79 rifampicin
embB 4247431 p.Met306Ile missense_variant 0.85 ethambutol
gid 4408100 c.102delG frameshift_variant 0.9 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 0.87
gyrA 8135 c.834C>T synonymous_variant 0.18
gyrA 9304 p.Gly668Asp missense_variant 0.91
rpoC 765150 p.Gly594Glu missense_variant 0.89
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303601 p.Glu224Gly missense_variant 0.82
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.39
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168149 p.Pro822Ser missense_variant 0.19
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 0.89
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.85
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.91
embB 4249408 c.2895G>A synonymous_variant 0.86
aftB 4269540 c.-704C>T upstream_gene_variant 0.9
whiB6 4338595 c.-75delG upstream_gene_variant 1.0