Run ID: SRR5341398
Sample name:
Date: 20-10-2023 18:52:54
Number of reads: 1715335
Percentage reads mapped: 99.51
Strain: lineage4.1.1.3;lineage3
Drug-resistance: Pre-XDR-TB
Drug | Resistance | Supporting mutations |
---|---|---|
Rifampicin | R | rpoB p.Ser450Leu (1.00) |
Isoniazid | R | fabG1 c.-15C>T (0.50), katG p.Ser315Thr (1.00) |
Ethambutol | R | embB p.Met306Ile (0.64), embB p.Tyr319Ser (0.33) |
Pyrazinamide | R | pncA c.382dupG (0.61) |
Streptomycin | R | gid p.Gln125* (0.33) |
Fluoroquinolones | R | gyrA p.Ala90Val (0.62) |
Moxifloxacin | R | gyrA p.Ala90Val (0.62) |
Ofloxacin | R | gyrA p.Ala90Val (0.62) |
Levofloxacin | R | gyrA p.Ala90Val (0.62) |
Ciprofloxacin | R | gyrA p.Ala90Val (0.62) |
Aminoglycosides | ||
Amikacin | ||
Capreomycin | ||
Kanamycin | ||
Cycloserine | ||
Ethionamide | R | fabG1 c.-15C>T (0.50) |
Clofazimine | ||
Para-aminosalicylic_acid | ||
Delamanid | ||
Bedaquiline | ||
Linezolid |
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage3 | East-African-Indian | CAS | RD750 | 0.63 |
lineage4 | Euro-American | LAM;T;S;X;H | None | 0.31 |
lineage4.1 | Euro-American | T;X;H | None | 0.36 |
lineage4.1.1 | Euro-American (X-type) | X1;X2;X3 | None | 0.37 |
lineage4.1.1.3 | Euro-American (X-type) | X1;X3 | RD193 | 0.33 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
gyrA | 7570 | p.Ala90Val | missense_variant | 0.62 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin |
fabG1 | 1673425 | c.-15C>T | upstream_gene_variant | 0.5 | isoniazid, ethionamide |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
pncA | 2288859 | c.382dupG | frameshift_variant | 0.61 | pyrazinamide |
embB | 4247431 | p.Met306Ile | missense_variant | 0.64 | ethambutol |
embB | 4247469 | p.Tyr319Ser | missense_variant | 0.33 | ethambutol |
gid | 4407830 | p.Gln125* | stop_gained | 0.33 | streptomycin |
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 | 0.55 |
rpoB | 759746 | c.-61C>T | upstream_gene_variant | 0.6 |
rpoB | 761993 | c.2187C>T | synonymous_variant | 0.7 |
rpoC | 762434 | c.-936T>G | upstream_gene_variant | 0.57 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 0.84 |
rpoC | 764819 | p.Trp484Gly | missense_variant | 0.67 |
rpoC | 765150 | p.Gly594Glu | missense_variant | 0.39 |
rpoC | 766196 | p.Asp943Asn | missense_variant | 0.34 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 0.7 |
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 | 1.0 |
katG | 2153915 | p.Asn733Asp | missense_variant | 0.42 |
katG | 2154724 | p.Arg463Leu | missense_variant | 0.75 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 0.57 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2289047 | c.195C>T | synonymous_variant | 0.58 |
pncA | 2289365 | c.-125delC | upstream_gene_variant | 0.73 |
ahpC | 2726105 | c.-88G>A | upstream_gene_variant | 0.61 |
folC | 2747466 | c.130_132dupGAT | conservative_inframe_insertion | 0.76 |
Rv2752c | 3064991 | p.Arg401Gly | missense_variant | 0.55 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
alr | 3841473 | c.-53G>A | upstream_gene_variant | 0.69 |
embC | 4242075 | p.Arg738Gln | missense_variant | 0.66 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embC | 4242803 | p.Val981Leu | missense_variant | 0.41 |
embB | 4249408 | c.2895G>A | synonymous_variant | 0.33 |
ubiA | 4269320 | p.Leu172Val | missense_variant | 0.39 |
ethR | 4327691 | p.Asp48Gly | missense_variant | 0.43 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407588 | c.615A>G | synonymous_variant | 0.63 |
gid | 4408123 | c.79delG | frameshift_variant | 0.56 |