Run ID: ERR8025686
Sample name:
Date: 20-05-2023 20:47:39
Number of reads: 3035814
Percentage reads mapped: 99.6
Strain: lineage2.2.2
Drug-resistance: Pre-XDR-TB
Drug | Resistance | Supporting mutations |
---|---|---|
Rifampicin | R | rpoB p.Asp435Val (1.00) |
Isoniazid | R | fabG1 c.-17G>T (1.00), katG p.Ser315Thr (1.00) |
Ethambutol | R | embB p.Met306Ile (1.00) |
Pyrazinamide | R | pncA c.517dupG (1.00), pncA c.517dupG (1.00) |
Streptomycin | R | rrs n.514A>C (1.00), gid p.Leu79Ser (1.00) |
Fluoroquinolones | R | gyrA p.Asp94Asn (0.97) |
Moxifloxacin | R | gyrA p.Asp94Asn (0.97) |
Ofloxacin | R | gyrA p.Asp94Asn (0.97) |
Levofloxacin | R | gyrA p.Asp94Asn (0.97) |
Ciprofloxacin | R | gyrA p.Asp94Asn (0.97) |
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 | fabG1 c.-17G>T (1.00), ethA p.Ala381Pro (1.00) |
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 | 7581 | p.Asp94Asn | missense_variant | 0.97 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761110 | p.Asp435Val | 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 |
fabG1 | 1673423 | c.-17G>T | upstream_gene_variant | 1.0 | isoniazid, ethionamide |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
pncA | 2288724 | c.517dupG | frameshift_variant | 1.0 | pyrazinamide, pyrazinamide |
embB | 4247431 | p.Met306Ile | missense_variant | 1.0 | ethambutol |
ethA | 4326333 | p.Ala381Pro | missense_variant | 1.0 | ethionamide |
gid | 4407967 | p.Leu79Ser | missense_variant | 1.0 | streptomycin |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 7252 | c.2015delT | frameshift_variant | 0.11 |
gyrA | 7273 | c.-29C>T | upstream_gene_variant | 0.11 |
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 | 491138 | c.359delG | frameshift_variant | 0.17 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 |
rpoB | 760943 | c.1137C>A | synonymous_variant | 0.12 |
rpoB | 762763 | p.Thr986Lys | missense_variant | 0.12 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
rpoC | 765880 | p.Lys837Asn | missense_variant | 0.12 |
rpoC | 765956 | c.2588_2589dupCC | frameshift_variant | 0.12 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 |
mmpS5 | 778787 | c.118delA | frameshift_variant | 0.13 |
mmpR5 | 779278 | p.Pro97Ala | missense_variant | 0.1 |
mmpR5 | 779371 | p.Ala128Thr | missense_variant | 0.19 |
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 1.0 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
Rv1258c | 1406625 | p.Tyr239Cys | missense_variant | 0.12 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1473316 | n.1471C>A | non_coding_transcript_exon_variant | 0.12 |
rrl | 1474823 | n.1166C>T | non_coding_transcript_exon_variant | 0.13 |
rrl | 1475440 | n.1783T>A | non_coding_transcript_exon_variant | 0.11 |
rrl | 1476099 | n.2442A>G | non_coding_transcript_exon_variant | 0.11 |
rrl | 1476318 | n.2661T>C | non_coding_transcript_exon_variant | 0.1 |
inhA | 1674554 | c.356dupG | frameshift_variant | 0.1 |
rpsA | 1834177 | c.636A>C | synonymous_variant | 1.0 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
ndh | 2101767 | p.Arg426Gly | missense_variant | 0.1 |
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
PPE35 | 2170772 | c.-160C>T | upstream_gene_variant | 0.17 |
Rv1979c | 2221939 | p.Arg409Gln | missense_variant | 1.0 |
Rv1979c | 2223022 | c.141_142delGC | frameshift_variant | 0.14 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
thyX | 3067771 | p.Gly59Ser | missense_variant | 0.12 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
ald | 3086995 | p.Gly59Asp | missense_variant | 0.12 |
fbiD | 3339175 | p.Ala20Thr | missense_variant | 0.11 |
Rv3083 | 3449036 | p.Lys178Met | missense_variant | 0.11 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
Rv3236c | 3612178 | c.939C>T | synonymous_variant | 0.15 |
Rv3236c | 3612797 | p.Ala107Val | missense_variant | 0.12 |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 1.0 |
alr | 3840307 | p.Gly372Cys | missense_variant | 0.33 |
alr | 3840586 | p.Cys279Arg | missense_variant | 0.12 |
rpoA | 3877665 | c.843C>A | synonymous_variant | 0.14 |
clpC1 | 4040142 | p.Asp188Val | missense_variant | 0.11 |
panD | 4044412 | c.-131C>T | upstream_gene_variant | 0.12 |
panD | 4044436 | c.-155C>T | upstream_gene_variant | 0.12 |
embC | 4239778 | c.-85C>T | upstream_gene_variant | 0.18 |
embC | 4240147 | c.285C>A | synonymous_variant | 0.12 |
embC | 4240570 | c.712delG | frameshift_variant | 0.18 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243460 | c.228C>T | synonymous_variant | 1.0 |
embA | 4245907 | p.Leu892Pro | missense_variant | 0.12 |
embB | 4246796 | p.Gly95Ser | missense_variant | 0.14 |
aftB | 4267346 | c.1490delA | frameshift_variant | 0.15 |
aftB | 4267647 | p.Asp397Gly | missense_variant | 1.0 |
aftB | 4268755 | p.Ala28Thr | missense_variant | 0.12 |
ubiA | 4269967 | c.-135delG | upstream_gene_variant | 0.17 |
ethR | 4327291 | c.-258C>G | upstream_gene_variant | 0.11 |
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 |