Run ID: ERR5865320
Sample name:
Date: 01-04-2023 23:56:36
Number of reads: 638667
Percentage reads mapped: 99.33
Strain: lineage2.2
Drug-resistance: Pre-XDR-TB
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage2 | East-Asian | Beijing | RD105 | 0.99 |
lineage2.2 | East-Asian (Beijing) | Beijing-RD207 | RD105;RD207 | 1.0 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
gyrA | 7570 | p.Ala90Val | missense_variant | 1.0 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
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 |
fabG1 | 1673425 | c.-15C>T | upstream_gene_variant | 1.0 | isoniazid, ethionamide |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
pncA | 2288697 | p.Leu182Trp | missense_variant | 1.0 | pyrazinamide |
eis | 2715369 | c.-37G>T | upstream_gene_variant | 1.0 | kanamycin |
folC | 2747141 | p.Glu153Gly | missense_variant | 1.0 | para-aminosalicylic_acid |
embB | 4247431 | p.Met306Ile | missense_variant | 1.0 | ethambutol |
ethA | 4327172 | c.301delC | frameshift_variant | 1.0 | ethionamide |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrA | 6550 | c.-752A>T | upstream_gene_variant | 0.25 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 8078 | c.777A>G | synonymous_variant | 0.11 |
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 |
rpoB | 762793 | p.Val996Asp | missense_variant | 0.2 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
rpoC | 765462 | p.Asn698Ser | missense_variant | 0.94 |
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 | 779086 | p.Thr33Ala | missense_variant | 0.4 |
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 |
Rv1258c | 1407101 | c.240G>A | synonymous_variant | 0.12 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1471823 | n.-22delT | upstream_gene_variant | 0.18 |
rpsA | 1834177 | c.636A>C | synonymous_variant | 1.0 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
ndh | 2102201 | p.Ser281* | stop_gained | 0.12 |
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
PPE35 | 2169016 | p.Thr533Ala | missense_variant | 1.0 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
kasA | 2518916 | p.Ala268Thr | missense_variant | 0.15 |
folC | 2746747 | c.852G>C | synonymous_variant | 1.0 |
folC | 2746880 | p.Lys240Arg | missense_variant | 0.18 |
folC | 2747615 | c.-17C>A | upstream_gene_variant | 0.12 |
ribD | 2987021 | c.183G>C | synonymous_variant | 0.14 |
thyX | 3067947 | c.-2C>A | upstream_gene_variant | 0.22 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
Rv3083 | 3448584 | c.81C>T | synonymous_variant | 0.2 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
fprA | 3474652 | p.Ala216Ser | missense_variant | 0.1 |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 1.0 |
fbiB | 3642561 | p.Asp343Asn | missense_variant | 0.18 |
embC | 4240576 | c.714A>T | synonymous_variant | 0.12 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 0.93 |
embC | 4243018 | p.Asp1052Glu | missense_variant | 0.11 |
embA | 4243460 | c.228C>T | synonymous_variant | 1.0 |
embB | 4246548 | p.Pro12Gln | missense_variant | 0.12 |
embB | 4246555 | c.42G>C | synonymous_variant | 0.13 |
embB | 4246556 | p.Ala15Pro | missense_variant | 0.13 |
aftB | 4267647 | p.Asp397Gly | missense_variant | 1.0 |
aftB | 4268026 | p.Val271Met | missense_variant | 0.12 |
ethR | 4327012 | c.-537C>T | upstream_gene_variant | 0.13 |
gid | 4407588 | c.615A>G | synonymous_variant | 1.0 |
gid | 4407927 | p.Glu92Asp | missense_variant | 1.0 |