Run ID: SRR25206953
Sample name:
Date: 12-02-2024 13:30:01
Number of reads: 6326064
Percentage reads mapped: 99.54
Strain: lineage2.2.1
Drug-resistance: XDR-TB
Drug | Resistance | Supporting mutations |
---|---|---|
Rifampicin | R | rpoB p.Ala286Val (1.00), rpoB p.Ser450Leu (1.00) |
Isoniazid | R | katG p.Ser315Thr (1.00) |
Ethambutol | R | embB p.Met306Ile (1.00) |
Pyrazinamide | R | pncA p.Gly132Asp (1.00) |
Streptomycin | R | rpsL p.Lys88Arg (1.00) |
Fluoroquinolones | R | gyrB p.Asp461Ala (0.16), gyrA p.Ser91Pro (0.84), gyrA p.Asp94Ala (1.00) |
Moxifloxacin | R | gyrB p.Asp461Ala (0.16), gyrA p.Ser91Pro (0.84), gyrA p.Asp94Ala (1.00) |
Ofloxacin | R | gyrB p.Asp461Ala (0.16), gyrA p.Ser91Pro (0.84), gyrA p.Asp94Ala (1.00) |
Levofloxacin | R | gyrB p.Asp461Ala (0.16), gyrA p.Ser91Pro (0.84), gyrA p.Asp94Ala (1.00) |
Ciprofloxacin | R | gyrB p.Asp461Ala (0.16), gyrA p.Ser91Pro (0.84), gyrA p.Asp94Ala (1.00) |
Aminoglycosides | R | rrs n.1401A>G (0.13), rrs n.1484G>T (0.86) |
Amikacin | R | rrs n.1401A>G (0.13), rrs n.1484G>T (0.86) |
Capreomycin | R | rrs n.1401A>G (0.13), rrs n.1484G>T (0.86) |
Kanamycin | R | rrs n.1401A>G (0.13), rrs n.1484G>T (0.86) |
Cycloserine | R | alr p.Leu113Arg (0.48) |
Ethionamide | ||
Clofazimine | R | mmpR5 p.Arg134* (0.17) |
Para-aminosalicylic_acid | R | thyA p.Arg235Pro (1.00) |
Delamanid | ||
Bedaquiline | R | mmpR5 p.Arg134* (0.17) |
Linezolid |
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage2 | East-Asian | Beijing | RD105 | 1.0 |
lineage2.2 | East-Asian (Beijing) | Beijing-RD207 | RD105;RD207 | 1.0 |
lineage2.2.1 | East-Asian (Beijing) | Beijing-RD181 | RD105;RD207;RD181 | 1.0 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
gyrB | 6621 | p.Asp461Ala | missense_variant | 0.16 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
gyrA | 7572 | p.Ser91Pro | missense_variant | 0.84 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
gyrA | 7582 | p.Asp94Ala | missense_variant | 1.0 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 760663 | p.Ala286Val | missense_variant | 1.0 | rifampicin |
rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin |
mmpR5 | 779389 | p.Arg134* | stop_gained | 0.17 | clofazimine, bedaquiline |
rpsL | 781822 | p.Lys88Arg | missense_variant | 1.0 | streptomycin |
rrs | 1473246 | n.1401A>G | non_coding_transcript_exon_variant | 0.13 | kanamycin, capreomycin, aminoglycosides, amikacin |
rrs | 1473329 | n.1484G>T | non_coding_transcript_exon_variant | 0.86 | kanamycin, capreomycin, aminoglycosides, amikacin |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
pncA | 2288847 | p.Gly132Asp | missense_variant | 1.0 | pyrazinamide |
thyA | 3073768 | p.Arg235Pro | missense_variant | 1.0 | para-aminosalicylic_acid |
alr | 3841083 | p.Leu113Arg | missense_variant | 0.48 | cycloserine |
embB | 4247431 | p.Met306Ile | missense_variant | 1.0 | ethambutol |
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 |
mshA | 575907 | p.Ala187Val | missense_variant | 1.0 |
ccsA | 620625 | p.Ile245Met | missense_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 | 0.99 |
mmpL5 | 776182 | p.Asp767Asn | missense_variant | 1.0 |
mmpR5 | 779111 | p.Gly41Val | missense_variant | 0.48 |
mmpR5 | 779137 | p.Arg50Gly | missense_variant | 0.37 |
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 1.0 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
Rv1258c | 1406760 | c.580_581insC | frameshift_variant | 1.0 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrl | 1475953 | n.2296A>C | non_coding_transcript_exon_variant | 0.15 |
rpsA | 1834177 | c.636A>C | synonymous_variant | 1.0 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
thyX | 3067954 | c.-9G>A | upstream_gene_variant | 1.0 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 1.0 |
alr | 3840259 | p.Tyr388Asp | missense_variant | 0.49 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243460 | c.228C>T | synonymous_variant | 1.0 |
aftB | 4267647 | p.Asp397Gly | missense_variant | 1.0 |
ethA | 4327370 | p.Leu35Arg | missense_variant | 1.0 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407588 | c.615A>G | synonymous_variant | 1.0 |
gid | 4407927 | p.Glu92Asp | missense_variant | 1.0 |