Run ID: ERR5864538
Sample name:
Date: 01-04-2023 23:24:59
Number of reads: 1074897
Percentage reads mapped: 99.41
Strain: lineage2.2.1
Drug-resistance: Pre-XDR-TB
Drug | Resistance | Supporting mutations |
---|
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 |
---|---|---|---|---|---|
gyrB | 6750 | p.Ala504Val | missense_variant | 0.97 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin |
rrs | 1472362 | n.517C>T | non_coding_transcript_exon_variant | 1.0 | streptomycin |
inhA | 1674048 | c.-154G>A | upstream_gene_variant | 1.0 | isoniazid, ethionamide |
tlyA | 1918696 | c.759delC | frameshift_variant | 0.1 | capreomycin, capreomycin |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
pncA | 2289222 | p.Val7Ala | missense_variant | 0.95 | pyrazinamide |
eis | 2715346 | c.-14C>T | upstream_gene_variant | 1.0 | kanamycin, amikacin |
embB | 4247429 | p.Met306Val | missense_variant | 1.0 | ethambutol |
ethA | 4326705 | c.768delG | frameshift_variant | 1.0 | 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 | 7707 | p.Pro136Thr | missense_variant | 0.11 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 |
mshA | 575371 | c.24C>T | synonymous_variant | 0.11 |
mshA | 575907 | p.Ala187Val | missense_variant | 1.0 |
ccsA | 620625 | p.Ile245Met | missense_variant | 1.0 |
ccsA | 620645 | p.Glu252Val | missense_variant | 0.12 |
rpoB | 762574 | p.Gly923Asp | missense_variant | 0.13 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
rpoB | 763159 | p.Leu1118Pro | missense_variant | 0.1 |
rpoC | 764817 | p.Val483Gly | missense_variant | 0.96 |
rpoC | 765971 | p.Ala868Thr | missense_variant | 0.12 |
rpoC | 766645 | p.Glu1092Asp | missense_variant | 0.95 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 |
mmpL5 | 776182 | p.Asp767Asn | missense_variant | 1.0 |
mmpL5 | 776932 | p.Asp517Tyr | missense_variant | 0.11 |
mmpR5 | 779254 | c.267delG | frameshift_variant | 0.11 |
mmpR5 | 779392 | p.Arg135Trp | missense_variant | 0.11 |
mmpS5 | 779585 | c.-680A>G | upstream_gene_variant | 0.18 |
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 1.0 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
rplC | 800894 | p.Val29Ala | missense_variant | 0.11 |
Rv1258c | 1406760 | c.580_581insC | frameshift_variant | 1.0 |
embR | 1417483 | c.-136A>G | upstream_gene_variant | 0.1 |
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 | 2154724 | p.Arg463Leu | missense_variant | 1.0 |
katG | 2155754 | p.Gly120Cys | missense_variant | 0.12 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
PPE35 | 2169032 | c.1581T>C | synonymous_variant | 0.12 |
PPE35 | 2170115 | c.498G>T | synonymous_variant | 0.11 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
kasA | 2518409 | p.Gly99Ser | missense_variant | 0.11 |
folC | 2746511 | p.Ala363Val | missense_variant | 0.15 |
ribD | 2987554 | p.Arg239Leu | missense_variant | 0.1 |
thyX | 3067356 | p.Ala197Val | missense_variant | 0.33 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
ald | 3087134 | p.Asp105Glu | missense_variant | 0.18 |
fbiD | 3339504 | p.Ile129Met | missense_variant | 1.0 |
Rv3083 | 3448307 | c.-197T>C | upstream_gene_variant | 0.1 |
Rv3083 | 3448497 | c.-7T>C | upstream_gene_variant | 0.12 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
whiB7 | 3568414 | p.Asp89Gly | missense_variant | 0.17 |
Rv3236c | 3612136 | c.981C>T | synonymous_variant | 0.12 |
Rv3236c | 3612220 | c.897T>C | synonymous_variant | 0.11 |
Rv3236c | 3612244 | c.873T>C | synonymous_variant | 0.11 |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 1.0 |
fbiB | 3642776 | c.1242G>C | synonymous_variant | 0.2 |
panD | 4043960 | c.321delT | frameshift_variant | 0.17 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243460 | c.228C>T | synonymous_variant | 1.0 |
embA | 4243702 | c.473_489delGCGCCGGGACCCTGCCG | frameshift_variant | 0.11 |
embA | 4244572 | p.Arg447Leu | missense_variant | 0.11 |
embB | 4248041 | p.Ala510Thr | missense_variant | 0.17 |
embB | 4248601 | c.2088G>T | synonymous_variant | 0.12 |
embB | 4249810 | c.3297G>T | stop_lost&splice_region_variant | 0.15 |
aftB | 4267647 | p.Asp397Gly | missense_variant | 1.0 |
whiB6 | 4338510 | c.12T>C | synonymous_variant | 0.12 |
whiB6 | 4338563 | c.-42G>T | upstream_gene_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 |