Run ID: ERR10748243
Sample name:
Date: 31-03-2023 10:48:41
Number of reads: 1177335
Percentage reads mapped: 99.86
Strain: lineage2.2.1.1;lineage1.2.2.1
Drug-resistance: MDR-TB
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage2 | East-Asian | Beijing | RD105 | 0.42 |
lineage1 | Indo-Oceanic | EAI | RD239 | 0.59 |
lineage2.2 | East-Asian (Beijing) | Beijing-RD207 | RD105;RD207 | 0.43 |
lineage1.2.2 | Indo-Oceanic | EAI1 | RD239 | 0.65 |
lineage2.2.1 | East-Asian (Beijing) | Beijing-RD181 | RD105;RD207;RD181 | 0.43 |
lineage1.2.2.1 | Indo-Oceanic | NA | RD239 | 0.62 |
lineage2.2.1.1 | East-Asian (Beijing) | Beijing-RD150 | RD105;RD207;RD181;RD150 | 0.38 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
rpoB | 761139 | p.His445Cys | missense_variant | 0.63 | rifampicin |
rpoB | 761161 | p.Leu452Pro | missense_variant | 0.35 | rifampicin |
katG | 2155168 | p.Ser315Asn | missense_variant | 1.0 | isoniazid |
pncA | 2289177 | c.64delA | frameshift_variant | 0.52 | pyrazinamide, pyrazinamide |
embB | 4247429 | p.Met306Val | missense_variant | 0.8 | ethambutol |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 5075 | c.-165C>T | upstream_gene_variant | 0.73 |
gyrB | 6112 | p.Met291Ile | missense_variant | 0.62 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 8452 | p.Ala384Val | missense_variant | 0.61 |
gyrA | 9143 | c.1842T>C | synonymous_variant | 0.59 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
fgd1 | 491060 | p.Met93Thr | missense_variant | 0.54 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 |
mshA | 575907 | p.Ala187Val | missense_variant | 0.3 |
ccsA | 620625 | p.Ile245Met | missense_variant | 0.44 |
ccsA | 620659 | p.Arg257Cys | missense_variant | 0.57 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
rpoC | 763884 | p.Ala172Val | missense_variant | 0.54 |
rpoC | 763886 | c.517C>A | synonymous_variant | 0.57 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 |
mmpL5 | 776182 | p.Asp767Asn | missense_variant | 0.25 |
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 0.39 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
rplC | 800899 | p.Ala31Thr | missense_variant | 0.57 |
Rv1258c | 1406760 | c.580_581insC | frameshift_variant | 0.15 |
embR | 1417019 | p.Cys110Tyr | missense_variant | 0.53 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1471842 | n.-4T>G | upstream_gene_variant | 0.74 |
rpsA | 1834177 | c.636A>C | synonymous_variant | 0.43 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
ndh | 2101848 | c.1195C>T | synonymous_variant | 0.53 |
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 |
katG | 2154977 | p.Ala379Thr | missense_variant | 0.43 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
Rv1979c | 2222308 | p.Asp286Gly | missense_variant | 0.7 |
Rv1979c | 2223014 | p.Tyr51Asn | missense_variant | 0.42 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
kasA | 2518132 | c.18C>T | synonymous_variant | 0.66 |
eis | 2714846 | p.Val163Ile | missense_variant | 0.26 |
ahpC | 2726051 | c.-142G>A | upstream_gene_variant | 0.66 |
ribD | 2987120 | c.282C>T | synonymous_variant | 0.7 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
Rv3083 | 3448714 | p.Asp71His | missense_variant | 0.71 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
fprA | 3474597 | c.591C>A | synonymous_variant | 0.62 |
fprA | 3474938 | p.Glu311Gly | missense_variant | 0.63 |
fprA | 3475159 | p.Asn385Asp | missense_variant | 0.52 |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 0.31 |
clpC1 | 4040517 | p.Val63Ala | missense_variant | 0.58 |
embC | 4240671 | p.Thr270Ile | missense_variant | 0.49 |
embC | 4240750 | c.888C>T | synonymous_variant | 0.67 |
embC | 4241042 | p.Asn394Asp | missense_variant | 0.62 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243225 | c.-8C>T | upstream_gene_variant | 0.38 |
embA | 4243460 | c.228C>T | synonymous_variant | 0.39 |
embA | 4245969 | p.Pro913Ser | missense_variant | 0.61 |
embB | 4247646 | p.Glu378Ala | missense_variant | 0.73 |
embB | 4248115 | c.1602C>T | synonymous_variant | 0.29 |
aftB | 4267647 | p.Asp397Gly | missense_variant | 0.49 |
ubiA | 4269387 | p.Glu149Asp | missense_variant | 0.73 |
aftB | 4269606 | c.-770T>C | upstream_gene_variant | 0.67 |
ethA | 4326439 | p.Asn345Lys | missense_variant | 0.63 |
ethR | 4327450 | c.-99G>A | upstream_gene_variant | 0.63 |
ethA | 4327602 | c.-129C>T | upstream_gene_variant | 0.59 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
whiB6 | 4338603 | c.-82C>T | upstream_gene_variant | 0.71 |
gid | 4407588 | c.615A>G | synonymous_variant | 1.0 |
gid | 4407873 | c.330G>T | synonymous_variant | 0.61 |
gid | 4407927 | p.Glu92Asp | missense_variant | 0.42 |