Run ID: ERR2510764
Sample name:
Date: 20-10-2023 06:29:57
Number of reads: 1388372
Percentage reads mapped: 90.97
Strain: lineage4.8
Drug-resistance: Pre-XDR-TB
Drug | Resistance | Supporting mutations |
---|---|---|
Rifampicin | R | rpoB p.Ser450Leu (1.00) |
Isoniazid | R | katG p.Ser315Thr (1.00) |
Ethambutol | R | embB p.Met306Val (1.00), embB p.Gly406Cys (1.00) |
Pyrazinamide | R | pncA p.Trp68* (1.00) |
Streptomycin | R | rpsL p.Lys88Gln (1.00) |
Fluoroquinolones | R | gyrB p.Asn499Thr (0.98) |
Moxifloxacin | R | gyrB p.Asn499Thr (0.98) |
Ofloxacin | R | gyrB p.Asn499Thr (0.98) |
Levofloxacin | R | gyrB p.Asn499Thr (0.98) |
Ciprofloxacin | R | gyrB p.Asn499Thr (0.98) |
Aminoglycosides | ||
Amikacin | ||
Capreomycin | ||
Kanamycin | ||
Cycloserine | ||
Ethionamide | R | ethA c.504delC (1.00) |
Clofazimine | ||
Para-aminosalicylic_acid | ||
Delamanid | ||
Bedaquiline | ||
Linezolid |
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage4 | Euro-American | LAM;T;S;X;H | None | 1.0 |
lineage4.8 | Euro-American (mainly T) | T1;T2;T3;T5 | RD219 | 1.0 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
gyrB | 6735 | p.Asn499Thr | missense_variant | 0.98 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin |
rpsL | 781821 | p.Lys88Gln | missense_variant | 1.0 | streptomycin |
katG | 2155167 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
pncA | 2289038 | p.Trp68* | stop_gained | 1.0 | pyrazinamide |
embB | 4247429 | p.Met306Val | missense_variant | 1.0 | ethambutol |
embB | 4247729 | p.Gly406Cys | missense_variant | 1.0 | ethambutol |
ethA | 4326969 | c.504delC | frameshift_variant | 1.0 | ethionamide |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 5078 | c.-162_-161insG | upstream_gene_variant | 0.36 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
rpoB | 759955 | p.Val50Gly | missense_variant | 1.0 |
rpoC | 765713 | p.Thr782Ala | 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 |
rrl | 1474001 | n.344C>T | non_coding_transcript_exon_variant | 1.0 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
ald | 3087251 | c.434dupG | frameshift_variant | 1.0 |
fbiA | 3640901 | p.Gln120Arg | missense_variant | 1.0 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
Rv3083 | 3448507 | c.5_*1408del | frameshift_variant&stop_lost&splice_region_variant | 1.0 |