Run ID: ERR4799481
Sample name:
Date: 20-10-2023 03:49:09
Number of reads: 3309967
Percentage reads mapped: 99.53
Strain: lineage3.1.2
Drug-resistance: Pre-XDR-TB
Drug | Resistance | Supporting mutations |
---|---|---|
Rifampicin | R | rpoB p.Asp435Val (0.98) |
Isoniazid | R | katG p.Ser315Thr (0.99) |
Ethambutol | ||
Pyrazinamide | ||
Streptomycin | ||
Fluoroquinolones | R | gyrA p.Ser91Pro (0.83) |
Moxifloxacin | R | gyrA p.Ser91Pro (0.83) |
Ofloxacin | R | gyrA p.Ser91Pro (0.83) |
Levofloxacin | R | gyrA p.Ser91Pro (0.83) |
Ciprofloxacin | R | gyrA p.Ser91Pro (0.83) |
Aminoglycosides | ||
Amikacin | ||
Capreomycin | ||
Kanamycin | ||
Cycloserine | ||
Ethionamide | R | ethA c.752dupG (0.85), ethA c.752dupG (0.85) |
Clofazimine | ||
Para-aminosalicylic_acid | ||
Delamanid | ||
Bedaquiline | ||
Linezolid |
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage3 | East-African-Indian | CAS | RD750 | 0.99 |
lineage3.1 | East-African-Indian | Non-CAS1-Delhi | RD750 | 0.98 |
lineage3.1.2 | East-African-Indian | CAS;CAS2 | RD750 | 0.97 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
gyrA | 7572 | p.Ser91Pro | missense_variant | 0.83 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761110 | p.Asp435Val | missense_variant | 0.98 | rifampicin |
katG | 2155168 | p.Ser315Thr | missense_variant | 0.99 | isoniazid |
ethA | 4326721 | c.752dupG | frameshift_variant | 0.85 | ethionamide, ethionamide |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 |
ccsA | 620782 | p.Ala298Ser | missense_variant | 0.98 |
rpoB | 759746 | c.-61C>T | upstream_gene_variant | 1.0 |
rpoC | 762434 | c.-936T>G | upstream_gene_variant | 1.0 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | 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 | 1471854 | n.9G>A | non_coding_transcript_exon_variant | 1.0 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
katG | 2154724 | p.Arg463Leu | missense_variant | 0.98 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
PPE35 | 2168604 | p.Pro670Leu | missense_variant | 0.99 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2289047 | c.195C>T | synonymous_variant | 0.99 |
pncA | 2289365 | c.-125delC | upstream_gene_variant | 1.0 |
ahpC | 2726105 | c.-88G>A | upstream_gene_variant | 1.0 |
thyX | 3067771 | p.Gly59Cys | missense_variant | 0.99 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
clpC1 | 4040110 | c.595C>A | synonymous_variant | 1.0 |
embC | 4242075 | p.Arg738Gln | missense_variant | 0.99 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embB | 4246810 | c.297G>C | synonymous_variant | 0.98 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407588 | c.615A>G | synonymous_variant | 0.99 |
gid | 4407762 | c.435_440dupGACGAA | disruptive_inframe_insertion | 1.0 |