Run ID: ERR5866377
Sample name:
Date: 02-04-2023 00:39:17
Number of reads: 877184
Percentage reads mapped: 97.27
Strain: lineage2.2.1
Drug-resistance: Pre-XDR-TB
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage2 | East-Asian | Beijing | RD105 | 0.97 |
lineage2.2 | East-Asian (Beijing) | Beijing-RD207 | RD105;RD207 | 0.99 |
lineage2.2.1 | East-Asian (Beijing) | Beijing-RD181 | RD105;RD207;RD181 | 0.99 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
gyrA | 7582 | p.Asp94Gly | missense_variant | 0.2 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin |
rpsL | 781687 | p.Lys43Arg | missense_variant | 0.92 | streptomycin |
katG | 2154045 | p.Trp689* | stop_gained | 0.14 | isoniazid |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
eis | 2715346 | c.-14C>T | upstream_gene_variant | 0.95 | kanamycin, amikacin |
embB | 4247730 | p.Gly406Ala | missense_variant | 1.0 | ethambutol |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 7757 | p.Phe152Leu | missense_variant | 0.12 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
fgd1 | 491481 | c.700delT | frameshift_variant | 0.15 |
fgd1 | 491632 | p.Trp284Arg | missense_variant | 0.11 |
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 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
rpoC | 766627 | c.3258G>T | synonymous_variant | 0.22 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 0.93 |
mmpL5 | 776182 | p.Asp767Asn | missense_variant | 1.0 |
mmpL5 | 776745 | p.Arg579Leu | missense_variant | 0.11 |
mmpL5 | 777010 | c.1470delA | frameshift_variant | 0.11 |
mmpL5 | 777185 | c.1296G>A | synonymous_variant | 0.11 |
mmpL5 | 777414 | p.Ala356Val | missense_variant | 0.11 |
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 1.0 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
fbiC | 1304021 | p.His364Leu | missense_variant | 0.2 |
fbiC | 1305037 | p.Arg703Trp | missense_variant | 0.12 |
Rv1258c | 1406760 | c.580_581insC | frameshift_variant | 1.0 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrl | 1474453 | n.796T>C | non_coding_transcript_exon_variant | 0.12 |
fabG1 | 1673378 | c.-62C>T | upstream_gene_variant | 0.13 |
fabG1 | 1673602 | p.Leu55Met | missense_variant | 0.2 |
fabG1 | 1673972 | p.Ala178Glu | missense_variant | 0.17 |
inhA | 1674305 | c.106_108delCTG | conservative_inframe_deletion | 0.15 |
rpsA | 1834177 | c.636A>C | synonymous_variant | 1.0 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
tlyA | 1918018 | p.Ile27Val | missense_variant | 1.0 |
ndh | 2102752 | p.Gln97His | missense_variant | 0.12 |
ndh | 2102974 | c.69G>A | synonymous_variant | 0.14 |
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 0.95 |
PPE35 | 2169797 | c.816G>T | synonymous_variant | 0.13 |
Rv1979c | 2223063 | c.102A>G | synonymous_variant | 0.17 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2289071 | p.His57Gln | missense_variant | 0.89 |
pncA | 2290078 | c.-837C>A | upstream_gene_variant | 0.29 |
kasA | 2518600 | c.486C>T | synonymous_variant | 0.17 |
kasA | 2518601 | p.Gly163Trp | missense_variant | 0.17 |
eis | 2715058 | p.Arg92His | missense_variant | 0.15 |
eis | 2715332 | p.Val1Leu | missense_variant | 0.94 |
eis | 2715533 | c.-201T>C | upstream_gene_variant | 0.12 |
ahpC | 2726516 | p.Phe108Leu | missense_variant | 0.12 |
folC | 2746598 | p.Thr334Ile | missense_variant | 0.18 |
Rv2752c | 3064698 | c.1494C>A | synonymous_variant | 0.18 |
Rv2752c | 3065518 | p.Leu225Pro | missense_variant | 1.0 |
Rv2752c | 3066102 | c.90C>T | synonymous_variant | 0.11 |
ald | 3086731 | c.-89A>G | upstream_gene_variant | 1.0 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
Rv3083 | 3449436 | c.933G>A | synonymous_variant | 0.12 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
fprA | 3475264 | c.1259dupC | frameshift_variant | 0.12 |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 1.0 |
fbiA | 3641382 | p.Cys280* | stop_gained | 0.18 |
fbiB | 3641952 | p.Leu140Val | missense_variant | 0.12 |
rpoA | 3877969 | p.Ala180Gly | missense_variant | 1.0 |
rpoA | 3878119 | c.388dupG | frameshift_variant | 0.12 |
ddn | 3987235 | p.Pro131Gln | missense_variant | 0.13 |
ddn | 3987267 | p.Arg142Ser | missense_variant | 0.15 |
panD | 4043917 | p.Ala122Glu | missense_variant | 0.14 |
embC | 4240049 | c.191delA | frameshift_variant | 0.33 |
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 | 4247666 | p.Trp385Arg | missense_variant | 0.1 |
embB | 4247987 | p.Val492Met | missense_variant | 0.11 |
aftB | 4267175 | c.1662C>T | synonymous_variant | 0.15 |
aftB | 4267647 | p.Asp397Gly | missense_variant | 1.0 |
aftB | 4268017 | p.Val274Leu | missense_variant | 0.1 |
aftB | 4268042 | c.795A>G | synonymous_variant | 0.1 |
aftB | 4268582 | c.255C>T | synonymous_variant | 0.14 |
ubiA | 4269943 | c.-111delG | upstream_gene_variant | 0.15 |
ethA | 4326155 | p.Leu440Pro | missense_variant | 1.0 |
whiB6 | 4338371 | p.Thr51Pro | missense_variant | 0.92 |
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 |