Run ID: ERR2515631
Sample name:
Date: 31-03-2023 21:02:09
Number of reads: 358782
Percentage reads mapped: 99.7
Strain: lineage2.2.1
Drug-resistance: MDR-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 |
---|---|---|---|---|---|
rpoB | 761095 | p.Leu430Pro | missense_variant | 1.0 | rifampicin |
rpsL | 781585 | p.Arg9His | missense_variant | 0.17 | streptomycin |
katG | 2154728 | c.1383delG | frameshift_variant | 0.11 | isoniazid |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrA | 6400 | c.-902C>T | upstream_gene_variant | 0.12 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 9027 | c.1729dupT | frameshift_variant | 0.15 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
fgd1 | 490934 | p.Ala51Val | missense_variant | 0.13 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 |
mshA | 575907 | p.Ala187Val | missense_variant | 1.0 |
mshA | 576756 | p.Arg470His | missense_variant | 0.25 |
ccsA | 620625 | p.Ile245Met | missense_variant | 1.0 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
rpoC | 764192 | p.Glu275* | stop_gained | 0.15 |
rpoC | 764223 | p.Lys285Met | missense_variant | 0.11 |
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 | 777254 | c.1227G>T | synonymous_variant | 0.12 |
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 1.0 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
rplC | 801272 | p.Ala155Val | missense_variant | 0.15 |
fbiC | 1302737 | c.-194C>A | upstream_gene_variant | 0.12 |
fbiC | 1302911 | c.-20T>C | upstream_gene_variant | 0.12 |
fbiC | 1303511 | c.582delT | frameshift_variant | 0.15 |
Rv1258c | 1406760 | c.580_581insC | frameshift_variant | 1.0 |
Rv1258c | 1407380 | c.-40C>A | upstream_gene_variant | 0.29 |
embR | 1417273 | c.75C>T | synonymous_variant | 0.11 |
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 |
tlyA | 1918161 | c.222G>C | synonymous_variant | 0.12 |
tlyA | 1918641 | c.702G>T | synonymous_variant | 0.11 |
ndh | 2102665 | c.377dupT | frameshift_variant | 0.11 |
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 |
PPE35 | 2167652 | c.2960delC | frameshift_variant | 0.18 |
PPE35 | 2167824 | p.Gly930Val | missense_variant | 0.14 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
PPE35 | 2168510 | c.2103C>T | synonymous_variant | 0.15 |
PPE35 | 2170220 | c.393C>T | synonymous_variant | 0.18 |
Rv1979c | 2222656 | p.Lys170Met | missense_variant | 0.11 |
Rv1979c | 2222832 | c.333T>C | synonymous_variant | 0.11 |
Rv1979c | 2222934 | c.231C>G | synonymous_variant | 0.13 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2290114 | c.-874delC | upstream_gene_variant | 0.13 |
kasA | 2518460 | c.347delT | frameshift_variant | 0.17 |
kasA | 2518491 | p.Tyr126Cys | missense_variant | 0.18 |
folC | 2747714 | c.-116G>A | upstream_gene_variant | 0.14 |
pepQ | 2860307 | p.Gly38Trp | missense_variant | 0.12 |
Rv2752c | 3064660 | p.Val511Ala | missense_variant | 0.1 |
Rv2752c | 3066368 | c.-177C>G | upstream_gene_variant | 0.12 |
thyA | 3074198 | p.Pro92Ser | missense_variant | 0.12 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
fbiD | 3339372 | c.255C>T | synonymous_variant | 0.17 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 1.0 |
fbiB | 3642747 | c.1214delC | frameshift_variant | 0.11 |
ddn | 3987291 | p.Glu150Gln | missense_variant | 0.11 |
clpC1 | 4038511 | p.Asp732Tyr | missense_variant | 0.18 |
embC | 4239743 | c.-120G>A | upstream_gene_variant | 0.11 |
embC | 4240555 | p.Met231Ile | missense_variant | 0.11 |
embC | 4241996 | p.Thr712Ala | missense_variant | 0.12 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243460 | c.228C>T | synonymous_variant | 1.0 |
embA | 4243888 | c.660delG | frameshift_variant | 0.12 |
embB | 4247084 | p.Asp191His | missense_variant | 0.1 |
embB | 4247895 | p.Pro461Gln | missense_variant | 0.12 |
embB | 4249118 | p.Asp869Asn | missense_variant | 0.18 |
embB | 4249221 | p.Ala903Asp | missense_variant | 0.14 |
embB | 4249497 | p.Pro995Leu | missense_variant | 0.17 |
aftB | 4267084 | p.His585Tyr | missense_variant | 0.15 |
aftB | 4267288 | p.His517Tyr | missense_variant | 0.12 |
aftB | 4267398 | p.Pro480Arg | missense_variant | 0.11 |
aftB | 4267594 | p.Ala415Thr | missense_variant | 0.29 |
aftB | 4267647 | p.Asp397Gly | missense_variant | 1.0 |
aftB | 4268545 | p.Leu98Ile | missense_variant | 0.4 |
aftB | 4268787 | p.Phe17Ser | missense_variant | 0.15 |
ubiA | 4269856 | c.-23G>T | upstream_gene_variant | 0.11 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
whiB6 | 4338684 | c.-163C>T | upstream_gene_variant | 0.12 |
gid | 4407588 | c.615A>G | synonymous_variant | 1.0 |
gid | 4407620 | p.Tyr195His | missense_variant | 1.0 |
gid | 4407927 | p.Glu92Asp | missense_variant | 1.0 |