Run ID: ERR5866345
Sample name:
Date: 02-04-2023 00:38:16
Number of reads: 1000183
Percentage reads mapped: 97.62
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 | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin |
rpsL | 781687 | p.Lys43Arg | missense_variant | 1.0 | streptomycin |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
pncA | 2289057 | p.Pro62Leu | missense_variant | 1.0 | pyrazinamide |
eis | 2715369 | c.-37G>T | upstream_gene_variant | 1.0 | kanamycin |
embB | 4247730 | p.Gly406Asp | 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 | 9034 | p.Arg578Gln | missense_variant | 0.95 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 |
mshA | 575907 | p.Ala187Val | missense_variant | 1.0 |
mshA | 576227 | p.Arg294Cys | missense_variant | 0.13 |
ccsA | 620625 | p.Ile245Met | missense_variant | 1.0 |
ccsA | 620759 | p.Arg290His | missense_variant | 0.14 |
rpoB | 761280 | p.Gly492Cys | missense_variant | 0.15 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
rpoC | 765765 | p.Ile799Asn | missense_variant | 0.11 |
rpoC | 766645 | p.Glu1092Asp | missense_variant | 1.0 |
rpoC | 767001 | p.Thr1211Lys | missense_variant | 0.2 |
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 |
fbiC | 1303990 | c.1064delG | frameshift_variant | 0.12 |
Rv1258c | 1406760 | c.580_581insC | frameshift_variant | 1.0 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
inhA | 1673463 | c.-739G>T | upstream_gene_variant | 0.1 |
inhA | 1674726 | c.525G>T | synonymous_variant | 0.13 |
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 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
PPE35 | 2170048 | p.Leu189Val | missense_variant | 0.14 |
PPE35 | 2170053 | p.Thr187Ser | missense_variant | 0.17 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2290228 | c.-988delT | upstream_gene_variant | 0.12 |
kasA | 2519153 | p.Ile347Val | missense_variant | 0.11 |
folC | 2746686 | p.Ala305Ser | missense_variant | 0.14 |
Rv2752c | 3066301 | c.-111delC | upstream_gene_variant | 0.15 |
thyX | 3067212 | p.Pro245Gln | missense_variant | 0.14 |
thyX | 3067412 | c.534C>A | synonymous_variant | 0.1 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
ald | 3086890 | p.Ala24Val | missense_variant | 0.11 |
ald | 3086915 | p.Glu32Asp | missense_variant | 0.11 |
fbiD | 3339322 | p.Ala69Thr | missense_variant | 0.12 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 1.0 |
rpoA | 3878639 | c.-132C>G | upstream_gene_variant | 1.0 |
clpC1 | 4038696 | p.Thr670Asn | missense_variant | 0.15 |
clpC1 | 4039149 | p.Ile519Asn | missense_variant | 0.13 |
clpC1 | 4039729 | p.Asp326Asn | missense_variant | 0.1 |
clpC1 | 4040092 | p.Ser205Thr | missense_variant | 0.13 |
embC | 4240890 | p.Trp343* | stop_gained | 0.12 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243460 | c.228C>T | synonymous_variant | 1.0 |
embA | 4244184 | p.Ser318Leu | missense_variant | 0.14 |
embA | 4244397 | p.Val389Met | missense_variant | 1.0 |
embB | 4245545 | c.-969C>A | upstream_gene_variant | 0.15 |
embB | 4245929 | c.-585C>A | upstream_gene_variant | 0.12 |
embB | 4246548 | p.Pro12Gln | missense_variant | 0.18 |
embB | 4246555 | c.42G>C | synonymous_variant | 0.19 |
embB | 4246556 | p.Ala15Pro | missense_variant | 0.19 |
embB | 4246563 | p.Leu17Trp | missense_variant | 0.18 |
embB | 4246567 | c.54G>T | synonymous_variant | 0.19 |
embB | 4246990 | c.477C>A | synonymous_variant | 0.12 |
aftB | 4267647 | p.Asp397Gly | missense_variant | 1.0 |
aftB | 4267671 | p.Ala389Val | missense_variant | 0.14 |
aftB | 4268599 | p.Glu80Lys | missense_variant | 0.15 |
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 |