Run ID: ERR4831563
Sample name:
Date: 01-04-2023 21:01:13
Number of reads: 1055636
Percentage reads mapped: 99.5
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 | 7582 | p.Asp94Gly | missense_variant | 1.0 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin |
rrs | 1472359 | n.514A>C | non_coding_transcript_exon_variant | 1.0 | streptomycin |
fabG1 | 1673425 | c.-15C>T | upstream_gene_variant | 1.0 | isoniazid, ethionamide |
pncA | 2288775 | c.459_466delCAGGGTGC | frameshift_variant | 1.0 | pyrazinamide, pyrazinamide |
thyX | 3067961 | c.-16C>T | upstream_gene_variant | 1.0 | para-aminosalicylic_acid |
embB | 4247429 | p.Met306Val | missense_variant | 1.0 | ethambutol |
ethA | 4327408 | c.65delA | frameshift_variant | 1.0 | ethionamide, ethionamide |
ethR | 4327831 | p.Ala95Thr | missense_variant | 1.0 | ethionamide |
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 |
ccsA | 620625 | p.Ile245Met | missense_variant | 1.0 |
rpoC | 762482 | c.-888C>T | upstream_gene_variant | 0.17 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
rpoC | 763555 | c.186C>T | synonymous_variant | 1.0 |
rpoC | 765619 | p.Glu750Asp | 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 | 776218 | p.Ala755Thr | missense_variant | 0.13 |
mmpS5 | 778979 | c.-74G>T | upstream_gene_variant | 1.0 |
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 | 0.19 |
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 | 0.52 |
PPE35 | 2170053 | p.Thr187Ser | missense_variant | 0.52 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
thyA | 3073846 | p.Tyr209Cys | missense_variant | 1.0 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
ald | 3087743 | c.924G>A | synonymous_variant | 0.12 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
Rv3236c | 3612746 | p.Val124Ala | missense_variant | 0.13 |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 1.0 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243460 | c.228C>T | synonymous_variant | 1.0 |
embB | 4246544 | p.Thr11Pro | missense_variant | 0.16 |
embB | 4246548 | p.Pro12Gln | missense_variant | 0.28 |
embB | 4246555 | c.42G>C | synonymous_variant | 0.31 |
embB | 4246556 | p.Ala15Pro | missense_variant | 0.31 |
aftB | 4267647 | p.Asp397Gly | missense_variant | 1.0 |
ethA | 4326031 | c.1443C>T | synonymous_variant | 0.12 |
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 |