Run ID: ERR8025532
Sample name:
Date: 18-05-2023 01:01:51
Number of reads: 2845413
Percentage reads mapped: 99.67
Strain: lineage2.2.2
Drug-resistance: Pre-XDR-TB
Drug | Resistance | Supporting mutations |
---|---|---|
Rifampicin | R | rpoB p.Ser450Leu (1.00) |
Isoniazid | R | fabG1 c.-15C>T (1.00), katG p.Ser315Thr (1.00) |
Ethambutol | R | embB p.Met306Ile (1.00) |
Pyrazinamide | R | pncA p.Cys14Arg (1.00) |
Streptomycin | R | rrs n.514A>C (1.00), gid p.Leu79Ser (1.00) |
Fluoroquinolones | R | gyrA p.Asp94His (1.00) |
Moxifloxacin | R | gyrA p.Asp94His (1.00) |
Ofloxacin | R | gyrA p.Asp94His (1.00) |
Levofloxacin | R | gyrA p.Asp94His (1.00) |
Ciprofloxacin | R | gyrA p.Asp94His (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 | fabG1 c.-15C>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.Asp94His | missense_variant | 1.0 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761155 | p.Ser450Leu | 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 | 1673425 | c.-15C>T | upstream_gene_variant | 1.0 | isoniazid, ethionamide |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
pncA | 2289202 | p.Cys14Arg | missense_variant | 1.0 | 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 | 6171 | p.His311Arg | missense_variant | 0.13 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7422 | p.Leu41Met | missense_variant | 0.13 |
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 |
rpoB | 762200 | c.2394C>A | synonymous_variant | 0.12 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
rpoB | 763189 | p.Asn1128Ser | missense_variant | 0.1 |
rpoC | 764817 | p.Val483Gly | missense_variant | 1.0 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 |
mmpL5 | 777021 | p.Pro487Leu | missense_variant | 0.12 |
mmpL5 | 777306 | p.Pro392His | missense_variant | 0.12 |
mmpL5 | 777560 | c.921C>A | synonymous_variant | 0.12 |
mmpR5 | 779449 | p.Leu154Met | missense_variant | 0.12 |
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 1.0 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
fbiC | 1304068 | p.Val380Ile | missense_variant | 0.11 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrl | 1475185 | n.1528T>C | non_coding_transcript_exon_variant | 0.13 |
rrl | 1476738 | n.3081C>A | non_coding_transcript_exon_variant | 0.22 |
fabG1 | 1674035 | p.Gln199Arg | missense_variant | 0.11 |
rpsA | 1834007 | p.Arg156Cys | missense_variant | 0.12 |
rpsA | 1834177 | c.636A>C | synonymous_variant | 1.0 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
ndh | 2101699 | c.1344G>A | synonymous_variant | 0.17 |
ndh | 2102971 | p.Phe24Leu | missense_variant | 0.12 |
ndh | 2103185 | c.-143A>G | upstream_gene_variant | 0.1 |
katG | 2154602 | p.Gly504Trp | missense_variant | 0.13 |
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
PPE35 | 2170053 | p.Thr187Ile | missense_variant | 0.13 |
Rv1979c | 2221736 | c.1429C>A | synonymous_variant | 0.12 |
Rv1979c | 2221939 | p.Arg409Gln | missense_variant | 1.0 |
Rv1979c | 2222476 | p.Tyr230Cys | missense_variant | 0.11 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pepQ | 2860097 | p.Asp108Tyr | missense_variant | 0.13 |
Rv2752c | 3065448 | c.744C>A | synonymous_variant | 0.14 |
Rv2752c | 3066128 | p.Gly22Cys | missense_variant | 0.14 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
fprA | 3473946 | c.-61T>C | upstream_gene_variant | 0.1 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
fprA | 3474455 | p.Ala150Val | missense_variant | 0.15 |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 1.0 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243297 | p.Ile22Thr | missense_variant | 0.11 |
embA | 4243460 | c.228C>T | synonymous_variant | 1.0 |
embA | 4245104 | p.Trp624Cys | missense_variant | 0.12 |
aftB | 4267647 | p.Asp397Gly | missense_variant | 1.0 |
ubiA | 4269089 | p.Ala249Thr | 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 |