Run ID: SRR25827482
Sample name:
Date: 15-03-2024 16:14:47
Number of reads: 4692008
Percentage reads mapped: 97.63
Strain: lineage2.2.1
Drug-resistance: XDR-TB
Drug | Resistance | Supporting mutations |
---|---|---|
Rifampicin | R | rpoB p.Ser450Leu (1.00) |
Isoniazid | R | katG p.Ser315Thr (1.00) |
Ethambutol | R | embA c.-16C>T (0.49), embB p.Met306Val (0.46) |
Pyrazinamide | R | pncA p.Thr177Pro (0.46), pncA p.Ile5Ser (0.47) |
Streptomycin | R | rpsL p.Lys43Arg (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 (0.42) |
Amikacin | R | rrs n.1401A>G (0.42) |
Capreomycin | R | rrs n.1401A>G (0.42) |
Kanamycin | R | rrs n.1401A>G (0.42), eis c.-12C>T (0.48) |
Cycloserine | ||
Ethionamide | R | ethA c.774dupG (0.44), ethA c.774dupG (0.44) |
Clofazimine | ||
Para-aminosalicylic_acid | R | thyX c.-16C>T (0.47), thyA p.Thr22Ala (1.00) |
Delamanid | ||
Bedaquiline | ||
Linezolid | R | rplC p.Cys154Arg (0.54) |
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 |
---|---|---|---|---|---|
gyrA | 7582 | p.Asp94Gly | missense_variant | 1.0 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin |
rpsL | 781687 | p.Lys43Arg | missense_variant | 1.0 | streptomycin |
rplC | 801268 | p.Cys154Arg | missense_variant | 0.54 | linezolid |
rrs | 1473246 | n.1401A>G | non_coding_transcript_exon_variant | 0.42 | kanamycin, capreomycin, aminoglycosides, amikacin |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
pncA | 2288713 | p.Thr177Pro | missense_variant | 0.46 | pyrazinamide |
pncA | 2289228 | p.Ile5Ser | missense_variant | 0.47 | pyrazinamide |
eis | 2715344 | c.-12C>T | upstream_gene_variant | 0.48 | kanamycin |
thyX | 3067961 | c.-16C>T | upstream_gene_variant | 0.47 | para-aminosalicylic_acid |
thyA | 3074408 | p.Thr22Ala | missense_variant | 1.0 | para-aminosalicylic_acid |
embA | 4243217 | c.-16C>T | upstream_gene_variant | 0.49 | ethambutol |
embB | 4247429 | p.Met306Val | missense_variant | 0.46 | ethambutol |
ethA | 4326699 | c.774dupG | frameshift_variant | 0.44 | ethionamide, 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 | 9304 | p.Gly668Asp | missense_variant | 1.0 |
fgd1 | 491290 | p.Val170Met | missense_variant | 0.52 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 |
mshA | 575907 | p.Ala187Val | missense_variant | 0.99 |
ccsA | 620625 | p.Ile245Met | missense_variant | 1.0 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
rpoC | 764840 | p.Ile491Ala | missense_variant | 0.43 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 |
mmpL5 | 776182 | p.Asp767Asn | missense_variant | 1.0 |
mmpR5 | 779130 | c.144dupC | frameshift_variant | 0.5 |
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 | 1475250 | n.1593C>A | non_coding_transcript_exon_variant | 0.45 |
rrl | 1475479 | n.1822C>T | non_coding_transcript_exon_variant | 0.54 |
rpsA | 1834177 | c.636A>C | synonymous_variant | 0.99 |
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 |
ribD | 2987506 | p.Leu223Arg | missense_variant | 0.15 |
thyX | 3067949 | c.-4C>T | upstream_gene_variant | 0.54 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
Rv3083 | 3449354 | c.852dupC | frameshift_variant | 0.52 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 1.0 |
embC | 4241022 | p.Ala387Val | missense_variant | 1.0 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243460 | c.228C>T | synonymous_variant | 1.0 |
embB | 4247015 | p.Ser168Ala | missense_variant | 0.25 |
embB | 4247847 | p.Gln445Arg | missense_variant | 0.48 |
aftB | 4267647 | p.Asp397Gly | missense_variant | 1.0 |
ethA | 4327472 | c.2T>C | start_lost | 0.53 |
whiB6 | 4338292 | p.Ala77Val | missense_variant | 0.56 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407588 | c.615A>G | synonymous_variant | 1.0 |
gid | 4407620 | p.Tyr195His | missense_variant | 1.0 |
gid | 4407927 | p.Glu92Asp | missense_variant | 1.0 |