Run ID: ERR4827428
Sample name:
Date: 01-04-2023 18:01:47
Number of reads: 1070301
Percentage reads mapped: 99.57
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 |
---|---|---|---|---|---|
gyrA | 7582 | p.Asp94Gly | missense_variant | 1.0 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761139 | p.His445Ser | 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 | 2288820 | p.Gln141Pro | missense_variant | 1.0 | pyrazinamide |
eis | 2715346 | c.-14C>T | upstream_gene_variant | 1.0 | kanamycin, amikacin |
embB | 4247431 | p.Met306Ile | missense_variant | 1.0 | ethambutol |
ethA | 4327363 | c.110delA | frameshift_variant | 1.0 | ethionamide, ethionamide |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 5465 | p.Glu76Lys | missense_variant | 0.22 |
gyrB | 7167 | p.Ala643Val | missense_variant | 0.17 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 7662 | p.Asn121Asp | missense_variant | 0.15 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 |
mshA | 575833 | c.486C>T | synonymous_variant | 0.11 |
mshA | 575907 | p.Ala187Val | missense_variant | 1.0 |
ccsA | 620625 | p.Ile245Met | missense_variant | 1.0 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 |
mmpL5 | 776182 | p.Asp767Asn | missense_variant | 1.0 |
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 |
atpE | 1461290 | c.246A>T | stop_lost&splice_region_variant | 0.13 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
fabG1 | 1673346 | c.-94C>G | upstream_gene_variant | 0.29 |
fabG1 | 1673349 | c.-91G>C | upstream_gene_variant | 0.29 |
fabG1 | 1673357 | c.-83G>A | upstream_gene_variant | 0.2 |
fabG1 | 1673359 | c.-81T>C | upstream_gene_variant | 0.22 |
fabG1 | 1673361 | c.-79C>G | upstream_gene_variant | 0.22 |
fabG1 | 1673380 | c.-60C>G | upstream_gene_variant | 0.42 |
rpsA | 1833490 | c.-52C>T | upstream_gene_variant | 0.14 |
rpsA | 1834177 | c.636A>C | synonymous_variant | 1.0 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
katG | 2154676 | p.Ala479Glu | missense_variant | 0.13 |
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
PPE35 | 2170048 | p.Leu189Val | missense_variant | 0.23 |
PPE35 | 2170053 | p.Thr187Ser | missense_variant | 0.21 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2289747 | c.-506A>T | upstream_gene_variant | 0.13 |
Rv2752c | 3067158 | c.-967G>A | upstream_gene_variant | 0.11 |
thyX | 3067540 | p.Ala136Thr | missense_variant | 0.17 |
thyX | 3067954 | c.-9G>A | upstream_gene_variant | 1.0 |
ald | 3086731 | c.-89A>G | upstream_gene_variant | 1.0 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 1.0 |
fbiB | 3642781 | p.Val416Asp | missense_variant | 0.13 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243346 | c.114A>G | synonymous_variant | 1.0 |
embA | 4243460 | c.228C>T | synonymous_variant | 1.0 |
embB | 4246544 | p.Thr11Pro | missense_variant | 0.25 |
embB | 4246548 | p.Pro12Gln | missense_variant | 0.36 |
embB | 4246555 | c.42G>C | synonymous_variant | 0.43 |
embB | 4246556 | p.Ala15Pro | missense_variant | 0.43 |
embB | 4246563 | p.Leu17Trp | missense_variant | 0.42 |
embB | 4246567 | c.54G>T | synonymous_variant | 0.38 |
embB | 4247024 | p.Pro171Ala | missense_variant | 0.29 |
embB | 4247028 | p.Leu172Gln | missense_variant | 0.4 |
embB | 4247450 | p.Ala313Pro | missense_variant | 0.17 |
aftB | 4267647 | p.Asp397Gly | missense_variant | 1.0 |
ethA | 4326289 | c.1185C>T | synonymous_variant | 0.11 |
whiB6 | 4338371 | p.Thr51Pro | 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 |