Run ID: SRR25827883
Sample name:
Date: 03-02-2024 00:13:02
Number of reads: 6864269
Percentage reads mapped: 99.1
Strain: lineage4.2.2.2;lineage3
Drug-resistance: Pre-XDR-TB
Drug | Resistance | Supporting mutations |
---|---|---|
Rifampicin | R | rpoB p.Asp435Tyr (0.55), rpoB p.Ser450Leu (0.48) |
Isoniazid | R | katG p.Ser315Thr (0.47), katG c.707_708delAC (0.53), ahpC c.-48G>A (0.48) |
Ethambutol | R | embB p.Gly406Ala (0.37), embB p.Asp1024Asn (0.50) |
Pyrazinamide | ||
Streptomycin | R | rpsL p.Lys43Arg (0.47) |
Fluoroquinolones | R | gyrA p.Ala90Val (0.47), gyrA p.Asp94Gly (0.51) |
Moxifloxacin | R | gyrA p.Ala90Val (0.47), gyrA p.Asp94Gly (0.51) |
Ofloxacin | R | gyrA p.Ala90Val (0.47), gyrA p.Asp94Gly (0.51) |
Levofloxacin | R | gyrA p.Ala90Val (0.47), gyrA p.Asp94Gly (0.51) |
Ciprofloxacin | R | gyrA p.Ala90Val (0.47), gyrA p.Asp94Gly (0.51) |
Aminoglycosides | ||
Amikacin | ||
Capreomycin | ||
Kanamycin | ||
Cycloserine | ||
Ethionamide | R | ethA p.Cys253* (0.46) |
Clofazimine | ||
Para-aminosalicylic_acid | ||
Delamanid | ||
Bedaquiline | ||
Linezolid |
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage3 | East-African-Indian | CAS | RD750 | 0.55 |
lineage4 | Euro-American | LAM;T;S;X;H | None | 0.48 |
lineage4.2 | Euro-American | H;T;LAM | None | 0.47 |
lineage4.2.2 | Euro-American (Ural) | T;LAM7-TUR | None | 0.44 |
lineage4.2.2.2 | Euro-American (Ural) | T;LAM7-TUR | None | 0.43 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
gyrA | 7570 | p.Ala90Val | missense_variant | 0.47 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
gyrA | 7582 | p.Asp94Gly | missense_variant | 0.51 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761109 | p.Asp435Tyr | missense_variant | 0.55 | rifampicin |
rpoB | 761155 | p.Ser450Leu | missense_variant | 0.48 | rifampicin |
rpsL | 781687 | p.Lys43Arg | missense_variant | 0.47 | streptomycin |
katG | 2155168 | p.Ser315Thr | missense_variant | 0.47 | isoniazid |
katG | 2155403 | c.707_708delAC | frameshift_variant | 0.53 | isoniazid |
ahpC | 2726145 | c.-48G>A | upstream_gene_variant | 0.48 | isoniazid |
embB | 4247730 | p.Gly406Ala | missense_variant | 0.37 | ethambutol |
embB | 4249583 | p.Asp1024Asn | missense_variant | 0.5 | ethambutol |
ethA | 4326715 | p.Cys253* | stop_gained | 0.46 | 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 | 8025 | p.Asp242His | missense_variant | 0.52 |
gyrA | 8158 | p.Ser286Leu | missense_variant | 0.54 |
gyrA | 8688 | p.Ala463Ser | missense_variant | 0.45 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 0.6 |
mshA | 576077 | c.730C>T | synonymous_variant | 0.48 |
rpoB | 759746 | c.-61C>T | upstream_gene_variant | 0.6 |
rpoB | 761489 | c.1683G>A | synonymous_variant | 0.48 |
rpoC | 762434 | c.-936T>G | upstream_gene_variant | 0.52 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 0.51 |
rpoC | 764916 | p.Leu516Pro | missense_variant | 0.48 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 0.53 |
mmpR5 | 779393 | p.Arg135Gln | missense_variant | 0.44 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
fbiC | 1305050 | p.Thr707Met | missense_variant | 0.43 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrl | 1476561 | n.2904C>T | non_coding_transcript_exon_variant | 0.62 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
katG | 2154724 | p.Arg463Leu | missense_variant | 0.57 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 0.61 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2289047 | c.195C>T | synonymous_variant | 0.45 |
pncA | 2289365 | c.-125delC | upstream_gene_variant | 0.56 |
ahpC | 2726105 | c.-88G>A | upstream_gene_variant | 0.53 |
ahpC | 2726116 | c.-77T>G | upstream_gene_variant | 0.53 |
Rv2752c | 3066280 | c.-89C>T | upstream_gene_variant | 0.39 |
ald | 3086742 | c.-78A>C | upstream_gene_variant | 0.41 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
whiB7 | 3568425 | c.255T>G | synonymous_variant | 0.14 |
whiB7 | 3568428 | c.252A>C | synonymous_variant | 0.18 |
embC | 4242075 | p.Arg738Gln | missense_variant | 0.64 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embB | 4247028 | p.Leu172Arg | missense_variant | 0.19 |
whiB6 | 4338399 | p.Trp41Cys | missense_variant | 0.5 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407588 | c.615A>G | synonymous_variant | 0.59 |
gid | 4408093 | p.Gly37Glu | missense_variant | 0.53 |