Run ID: ERR4799976
Sample name:
Date: 20-10-2023 04:03:15
Number of reads: 2823936
Percentage reads mapped: 99.55
Strain: lineage3.1.2
Drug-resistance: Pre-XDR-TB
Drug | Resistance | Supporting mutations |
---|---|---|
Rifampicin | R | rpoB p.Ser450Leu (1.00) |
Isoniazid | R | katG p.Ser315Thr (0.91) |
Ethambutol | R | embA c.-16C>T (0.96), embB p.Met306Ile (0.94) |
Pyrazinamide | ||
Streptomycin | R | rpsL p.Lys43Arg (0.99) |
Fluoroquinolones | R | gyrA p.Ala90Val (0.99) |
Moxifloxacin | R | gyrA p.Ala90Val (0.99) |
Ofloxacin | R | gyrA p.Ala90Val (0.99) |
Levofloxacin | R | gyrA p.Ala90Val (0.99) |
Ciprofloxacin | R | gyrA p.Ala90Val (0.99) |
Aminoglycosides | ||
Amikacin | ||
Capreomycin | ||
Kanamycin | ||
Cycloserine | ||
Ethionamide | ||
Clofazimine | ||
Para-aminosalicylic_acid | R | thyA c.-4520_*2087del (0.98) |
Delamanid | ||
Bedaquiline | ||
Linezolid |
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage3 | East-African-Indian | CAS | RD750 | 0.96 |
lineage3.1 | East-African-Indian | Non-CAS1-Delhi | RD750 | 0.97 |
lineage3.1.2 | East-African-Indian | CAS;CAS2 | RD750 | 0.96 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
gyrA | 7570 | p.Ala90Val | missense_variant | 0.99 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin |
rpsL | 781687 | p.Lys43Arg | missense_variant | 0.99 | streptomycin |
katG | 2155168 | p.Ser315Thr | missense_variant | 0.91 | isoniazid |
embA | 4243217 | c.-16C>T | upstream_gene_variant | 0.96 | ethambutol |
embB | 4247431 | p.Met306Ile | missense_variant | 0.94 | ethambutol |
thyA | 3071592 | c.-4520_*2087del | transcript_ablation | 0.98 | para-aminosalicylic_acid |
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 |
gyrA | 9758 | c.2457C>T | synonymous_variant | 0.96 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 0.98 |
rpoB | 759746 | c.-61C>T | upstream_gene_variant | 0.99 |
rpoC | 762434 | c.-936T>G | upstream_gene_variant | 1.0 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 0.97 |
rpoC | 767123 | p.Val1252Leu | missense_variant | 0.91 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 0.95 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 0.99 |
tlyA | 1918104 | c.165G>A | synonymous_variant | 0.94 |
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
PPE35 | 2168604 | p.Pro670Leu | missense_variant | 0.93 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2288929 | p.Gly105Cys | missense_variant | 0.94 |
pncA | 2289047 | c.195C>T | synonymous_variant | 0.99 |
pncA | 2289365 | c.-125delC | upstream_gene_variant | 0.98 |
ahpC | 2726105 | c.-88G>A | upstream_gene_variant | 0.96 |
ahpC | 2726773 | c.583dupG | frameshift_variant | 0.95 |
thyX | 3067948 | c.-3G>T | upstream_gene_variant | 0.97 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
fprA | 3474291 | c.285G>A | synonymous_variant | 0.97 |
clpC1 | 4040675 | c.30C>G | synonymous_variant | 0.97 |
embC | 4240256 | p.Leu132Ile | missense_variant | 0.99 |
embC | 4242075 | p.Arg738Gln | missense_variant | 0.99 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embB | 4247701 | p.Met396Ile | missense_variant | 0.94 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407588 | c.615A>G | synonymous_variant | 1.0 |