Run ID: SRR22873596
Sample name:
Date: 03-02-2024 04:39:19
Number of reads: 6976182
Percentage reads mapped: 99.67
Strain: lineage2.2.2
Drug-resistance: Pre-XDR-TB
Drug | Resistance | Supporting mutations |
---|---|---|
Rifampicin | R | rpoB p.Ile491Phe (1.00) |
Isoniazid | R | katG p.Ser315Thr (1.00) |
Ethambutol | R | embA c.-16C>G (0.99) |
Pyrazinamide | R | pncA p.Val44Gly (1.00) |
Streptomycin | R | rrs n.514A>C (1.00) |
Fluoroquinolones | R | gyrA p.Asp94Gly (1.00) |
Moxifloxacin | R | gyrA p.Asp94Gly (1.00) |
Ofloxacin | R | gyrA p.Asp94Gly (1.00) |
Levofloxacin | R | gyrA p.Asp94Gly (1.00) |
Ciprofloxacin | R | gyrA p.Asp94Gly (1.00) |
Aminoglycosides | R | rrs n.1401A>G (1.00) |
Amikacin | R | rrs n.1401A>G (1.00) |
Capreomycin | R | rrs n.1401A>G (1.00) |
Kanamycin | R | rrs n.1401A>G (1.00) |
Cycloserine | ||
Ethionamide | R | ethA c.672_673dupGC (0.66), ethA c.672_673dupGC (0.66) |
Clofazimine | ||
Para-aminosalicylic_acid | ||
Delamanid | ||
Bedaquiline | ||
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 |
lineage2.2.2 | East-Asian (Beijing) | Beijing-RD105/RD207 | RD105;RD207 | 1.0 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
gyrA | 7582 | p.Asp94Gly | missense_variant | 1.0 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761277 | p.Ile491Phe | missense_variant | 1.0 | rifampicin |
rrs | 1472359 | n.514A>C | non_coding_transcript_exon_variant | 1.0 | streptomycin |
rrs | 1473246 | n.1401A>G | non_coding_transcript_exon_variant | 1.0 | kanamycin, capreomycin, aminoglycosides, amikacin |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
pncA | 2289111 | p.Val44Gly | missense_variant | 1.0 | pyrazinamide |
embA | 4243217 | c.-16C>G | upstream_gene_variant | 0.99 | ethambutol |
ethA | 4326800 | c.672_673dupGC | frameshift_variant | 0.66 | ethionamide, ethionamide |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 6773 | p.Gly512Arg | missense_variant | 1.0 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 0.99 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 0.99 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 |
rpoB | 759940 | p.Pro45Leu | missense_variant | 1.0 |
rpoB | 759969 | p.Phe55Leu | 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 | 778976 | c.-496C>A | upstream_gene_variant | 1.0 |
mmpR5 | 779128 | c.140_142dupATC | disruptive_inframe_insertion | 0.58 |
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 1.0 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rpsA | 1834177 | c.636A>C | synonymous_variant | 1.0 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
katG | 2154159 | c.1953G>A | 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 |
folC | 2747481 | p.Glu40Lys | missense_variant | 0.93 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
Rv3083 | 3448902 | p.Cys133* | stop_gained | 0.99 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 0.99 |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 1.0 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243460 | c.228C>T | synonymous_variant | 1.0 |
embA | 4245519 | p.Pro763Ala | missense_variant | 1.0 |
embB | 4247874 | p.Ala454Val | missense_variant | 1.0 |
embB | 4249141 | c.2628G>C | synonymous_variant | 1.0 |
aftB | 4267647 | p.Asp397Gly | missense_variant | 1.0 |
ethA | 4326973 | p.Trp167* | stop_gained | 0.27 |
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 |