Run ID: ERR4827455
Sample name:
Date: 01-04-2023 18:04:12
Number of reads: 1835342
Percentage reads mapped: 99.41
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 |
rrs | 1473246 | n.1401A>G | non_coding_transcript_exon_variant | 1.0 | kanamycin, capreomycin, aminoglycosides, amikacin |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
pncA | 2288764 | p.Thr160Pro | missense_variant | 1.0 | pyrazinamide |
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 | 491742 | c.960T>C | synonymous_variant | 1.0 |
mshA | 575907 | p.Ala187Val | missense_variant | 1.0 |
mshA | 576098 | p.Asp251Ser | missense_variant | 1.0 |
mshA | 576102 | p.Arg252Pro | missense_variant | 1.0 |
mshA | 576104 | p.Arg253Ser | missense_variant | 1.0 |
mshA | 576405 | p.Glu353Val | missense_variant | 0.13 |
ccsA | 619727 | c.-164A>T | upstream_gene_variant | 0.4 |
ccsA | 620173 | p.Val95Ile | missense_variant | 0.15 |
ccsA | 620295 | c.405G>A | synonymous_variant | 0.12 |
ccsA | 620625 | p.Ile245Met | missense_variant | 1.0 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
rpoC | 766485 | p.Val1039Ala | missense_variant | 1.0 |
rpoC | 766645 | p.Glu1092Asp | missense_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 | 777164 | c.1317C>T | synonymous_variant | 0.14 |
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 1.0 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
Rv1258c | 1406760 | c.580_581insC | frameshift_variant | 1.0 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
fabG1 | 1673380 | c.-60C>G | upstream_gene_variant | 0.14 |
rpsA | 1834177 | c.636A>C | synonymous_variant | 1.0 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
ndh | 2102162 | p.Arg294Leu | missense_variant | 0.18 |
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
PPE35 | 2169902 | p.Leu237Phe | missense_variant | 0.16 |
PPE35 | 2169910 | p.Asn235Tyr | missense_variant | 0.17 |
PPE35 | 2170048 | p.Leu189Val | missense_variant | 0.15 |
PPE35 | 2170053 | p.Thr187Ser | missense_variant | 0.15 |
PPE35 | 2170415 | c.198A>C | synonymous_variant | 0.12 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
folC | 2746305 | p.Thr432Ser | missense_variant | 0.12 |
pepQ | 2859520 | p.Leu300Pro | missense_variant | 0.12 |
pepQ | 2859967 | p.Asp151Gly | missense_variant | 1.0 |
ribD | 2987092 | c.257dupG | frameshift_variant | 0.2 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
fprA | 3475292 | p.Phe429Ser | missense_variant | 0.14 |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 1.0 |
alr | 3840551 | c.870G>A | synonymous_variant | 0.12 |
alr | 3841546 | c.-126C>A | upstream_gene_variant | 0.24 |
embC | 4240801 | c.939C>T | synonymous_variant | 0.13 |
embC | 4240803 | p.Tyr314Phe | missense_variant | 0.13 |
embC | 4242116 | c.2256delC | frameshift_variant | 0.14 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4242661 | c.-572G>C | upstream_gene_variant | 0.22 |
embC | 4242710 | p.Gln950Glu | missense_variant | 0.17 |
embC | 4242920 | p.Ala1020Ser | missense_variant | 0.14 |
embA | 4243460 | c.228C>T | synonymous_variant | 1.0 |
embA | 4244865 | p.Ala545Pro | missense_variant | 0.12 |
embB | 4245662 | c.-852G>C | upstream_gene_variant | 0.12 |
embB | 4246544 | p.Thr11Pro | missense_variant | 0.33 |
embB | 4246548 | p.Pro12Gln | missense_variant | 0.3 |
embB | 4246555 | c.42G>C | synonymous_variant | 0.33 |
embB | 4246556 | p.Ala15Pro | missense_variant | 0.33 |
aftB | 4267647 | p.Asp397Gly | missense_variant | 1.0 |
aftB | 4268619 | p.Val73Gly | missense_variant | 0.25 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407585 | c.618A>C | synonymous_variant | 0.14 |
gid | 4407588 | c.615A>G | synonymous_variant | 1.0 |
gid | 4407927 | p.Glu92Asp | missense_variant | 1.0 |