Run ID: ERR5863865
Sample name:
Date: 01-04-2023 22:57:26
Number of reads: 703224
Percentage reads mapped: 99.12
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 | 7563 | p.Gly88Cys | missense_variant | 1.0 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761155 | p.Ser450Phe | missense_variant | 1.0 | rifampicin |
rpsL | 781687 | p.Lys43Arg | missense_variant | 1.0 | streptomycin |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
pncA | 2288820 | p.Gln141Pro | missense_variant | 1.0 | pyrazinamide |
eis | 2715369 | c.-37G>T | upstream_gene_variant | 1.0 | kanamycin |
embB | 4247429 | p.Met306Val | 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 | 9304 | p.Gly668Asp | missense_variant | 1.0 |
fgd1 | 491203 | c.422delA | frameshift_variant | 0.12 |
fgd1 | 491286 | c.504G>T | synonymous_variant | 0.15 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 |
mshA | 575691 | p.Gly115Val | missense_variant | 0.15 |
mshA | 575907 | p.Ala187Val | missense_variant | 1.0 |
mshA | 576111 | p.Ala255Asp | missense_variant | 0.17 |
mshA | 576219 | p.Pro291His | missense_variant | 0.18 |
mshA | 576454 | c.1107G>T | synonymous_variant | 0.17 |
mshA | 576557 | p.His404Asn | missense_variant | 0.25 |
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 |
mmpL5 | 777349 | p.Gly378Cys | missense_variant | 0.17 |
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 1.0 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
fbiC | 1302744 | c.-187C>A | upstream_gene_variant | 0.18 |
fbiC | 1302812 | c.-119G>A | upstream_gene_variant | 0.14 |
fbiC | 1303408 | p.Glu160* | stop_gained | 0.2 |
fbiC | 1303445 | p.Ser172Tyr | missense_variant | 0.18 |
fbiC | 1305313 | p.Arg795Ser | missense_variant | 0.17 |
Rv1258c | 1406760 | c.580_581insC | frameshift_variant | 0.93 |
Rv1258c | 1407203 | c.138C>A | synonymous_variant | 0.2 |
Rv1258c | 1407381 | c.-41G>T | upstream_gene_variant | 0.15 |
Rv1258c | 1407401 | c.-61G>T | upstream_gene_variant | 0.17 |
Rv1258c | 1407403 | c.-63G>T | upstream_gene_variant | 0.18 |
embR | 1416481 | c.867G>T | synonymous_variant | 0.17 |
embR | 1417077 | c.270delA | frameshift_variant | 0.11 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1472999 | n.1154C>T | non_coding_transcript_exon_variant | 0.22 |
rrl | 1473403 | n.-255C>A | upstream_gene_variant | 0.25 |
fabG1 | 1673668 | p.Glu77* | stop_gained | 0.18 |
rpsA | 1833767 | p.Pro76Thr | missense_variant | 0.14 |
rpsA | 1834177 | c.636A>C | synonymous_variant | 1.0 |
tlyA | 1917829 | c.-111C>A | upstream_gene_variant | 0.14 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
tlyA | 1917982 | p.Gly15Cys | missense_variant | 0.16 |
tlyA | 1918618 | p.Ala227Ser | missense_variant | 0.18 |
tlyA | 1918684 | c.745C>A | synonymous_variant | 0.15 |
ndh | 2101758 | p.Leu429Met | missense_variant | 0.13 |
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 |
katG | 2154770 | p.Asp448Tyr | missense_variant | 0.2 |
katG | 2154812 | p.Gln434Lys | missense_variant | 0.17 |
katG | 2156122 | c.-11G>T | upstream_gene_variant | 0.2 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
PPE35 | 2167960 | c.2652delG | frameshift_variant | 0.1 |
PPE35 | 2170331 | c.282G>T | synonymous_variant | 0.15 |
Rv1979c | 2221884 | c.1281G>A | synonymous_variant | 0.17 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
kasA | 2518234 | p.Glu40Asp | missense_variant | 0.29 |
ribD | 2986810 | c.-29C>A | upstream_gene_variant | 0.2 |
ribD | 2987253 | p.Ala139Ser | missense_variant | 0.15 |
Rv2752c | 3065150 | c.1041_1042insA | frameshift_variant | 1.0 |
Rv2752c | 3067187 | c.-997_-996insG | upstream_gene_variant | 1.0 |
thyX | 3067234 | p.Gly238Cys | missense_variant | 0.27 |
thyX | 3067244 | c.702C>T | synonymous_variant | 0.18 |
thyX | 3067256 | p.Phe230Leu | missense_variant | 0.25 |
ald | 3086731 | c.-89A>G | upstream_gene_variant | 1.0 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
Rv3083 | 3449560 | p.Leu353Met | missense_variant | 0.14 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
fprA | 3474117 | p.Asp37Glu | missense_variant | 0.13 |
whiB7 | 3568458 | c.222C>A | synonymous_variant | 0.17 |
whiB7 | 3568508 | p.Gln58Lys | missense_variant | 0.18 |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 1.0 |
fbiA | 3640600 | p.Gln20Lys | missense_variant | 0.18 |
rpoA | 3878256 | c.252G>T | synonymous_variant | 0.17 |
rpoA | 3878456 | c.52C>A | synonymous_variant | 0.18 |
clpC1 | 4038679 | p.Pro676Thr | missense_variant | 0.22 |
embC | 4240980 | p.Thr373Lys | 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 |
embA | 4243681 | p.Ala150Asp | missense_variant | 0.12 |
embA | 4245752 | p.Met840Ile | missense_variant | 0.14 |
embA | 4245882 | p.Gly884Cys | missense_variant | 0.2 |
embB | 4246427 | c.-87G>T | upstream_gene_variant | 0.15 |
embB | 4246920 | p.Pro136Gln | missense_variant | 0.17 |
embB | 4247043 | p.Pro177His | missense_variant | 0.14 |
embB | 4249731 | p.Ala1073Gly | missense_variant | 0.13 |
aftB | 4267647 | p.Asp397Gly | missense_variant | 1.0 |
aftB | 4267895 | p.Phe314Leu | missense_variant | 0.18 |
aftB | 4267970 | p.Phe289Leu | missense_variant | 0.17 |
ubiA | 4269893 | c.-60G>T | upstream_gene_variant | 0.2 |
ubiA | 4269995 | c.-162C>A | upstream_gene_variant | 0.17 |
ethA | 4328416 | c.-945_-944delTG | upstream_gene_variant | 0.14 |
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 | 4407873 | c.330G>T | synonymous_variant | 0.17 |
gid | 4407927 | p.Glu92Asp | missense_variant | 1.0 |