Run ID: ERR4799768
Sample name:
Date: 20-10-2023 04:09:51
Number of reads: 2597752
Percentage reads mapped: 99.63
Strain: lineage4.8
Drug-resistance: Pre-XDR-TB
Drug | Resistance | Supporting mutations |
---|---|---|
Rifampicin | R | rpoB p.Ser450Leu (1.00) |
Isoniazid | R | fabG1 c.-15C>T (0.96), katG p.Ser315Thr (0.94) |
Ethambutol | R | embB p.Met306Val (0.60), embB p.Gly406Asp (0.11), embB p.Gln497Arg (0.29) |
Pyrazinamide | ||
Streptomycin | ||
Fluoroquinolones | R | gyrA p.Ser91Pro (0.22), gyrA p.Asp94Gly (0.49) |
Moxifloxacin | R | gyrA p.Ser91Pro (0.22), gyrA p.Asp94Gly (0.49) |
Ofloxacin | R | gyrA p.Ser91Pro (0.22), gyrA p.Asp94Gly (0.49) |
Levofloxacin | R | gyrA p.Ser91Pro (0.22), gyrA p.Asp94Gly (0.49) |
Ciprofloxacin | R | gyrA p.Ser91Pro (0.22), gyrA p.Asp94Gly (0.49) |
Aminoglycosides | ||
Amikacin | ||
Capreomycin | ||
Kanamycin | ||
Cycloserine | ||
Ethionamide | R | fabG1 c.-15C>T (0.96) |
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 | 0.98 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
gyrA | 7572 | p.Ser91Pro | missense_variant | 0.22 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
gyrA | 7582 | p.Asp94Gly | missense_variant | 0.49 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin |
fabG1 | 1673425 | c.-15C>T | upstream_gene_variant | 0.96 | isoniazid, ethionamide |
katG | 2155168 | p.Ser315Thr | missense_variant | 0.94 | isoniazid |
embB | 4247429 | p.Met306Val | missense_variant | 0.6 | ethambutol |
embB | 4247730 | p.Gly406Asp | missense_variant | 0.11 | ethambutol |
embB | 4248003 | p.Gln497Arg | missense_variant | 0.29 | ethambutol |
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 |
rrl | 1474001 | n.344C>T | non_coding_transcript_exon_variant | 0.98 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
PPE35 | 2168149 | p.Pro822Ser | missense_variant | 0.98 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
clpC1 | 4039729 | p.Asp326Asn | missense_variant | 0.97 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
ethA | 4326632 | p.His281Arg | missense_variant | 0.99 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4408094 | p.Gly37Arg | missense_variant | 0.97 |
Rv3083 | 3448507 | c.5_*1408del | frameshift_variant&stop_lost&splice_region_variant | 0.99 |