Run ID: SRR7516439
Sample name:
Date: 04-04-2023 19:30:08
Number of reads: 2438232
Percentage reads mapped: 99.55
Strain: lineage4.2.1.1;lineage2.2.1
Drug-resistance: Pre-XDR-TB
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage2 | East-Asian | Beijing | RD105 | 0.8 |
lineage4 | Euro-American | LAM;T;S;X;H | None | 0.19 |
lineage4.2 | Euro-American | H;T;LAM | None | 0.17 |
lineage2.2 | East-Asian (Beijing) | Beijing-RD207 | RD105;RD207 | 0.79 |
lineage2.2.1 | East-Asian (Beijing) | Beijing-RD181 | RD105;RD207;RD181 | 0.8 |
lineage4.2.1 | Euro-American (TUR) | H3;H4 | None | 0.19 |
lineage4.2.1.1 | Euro-American (TUR) | H3;H4 | None | 0.18 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
gyrA | 7570 | p.Ala90Val | missense_variant | 0.87 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761095 | p.Leu430Pro | missense_variant | 0.78 | rifampicin |
rpoB | 761155 | p.Ser450Leu | missense_variant | 0.16 | rifampicin |
rpsL | 781687 | p.Lys43Arg | missense_variant | 0.64 | streptomycin |
rrs | 1472362 | n.517C>T | non_coding_transcript_exon_variant | 0.86 | streptomycin |
fabG1 | 1673425 | c.-15C>T | upstream_gene_variant | 0.77 | isoniazid, ethionamide |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
pncA | 2289252 | c.-11A>G | upstream_gene_variant | 0.27 | pyrazinamide |
eis | 2715369 | c.-37G>T | upstream_gene_variant | 0.76 | kanamycin |
embB | 4247553 | p.Ser347Ile | missense_variant | 0.81 | ethambutol |
embB | 4248003 | p.Gln497Arg | missense_variant | 0.36 | ethambutol |
ethA | 4327093 | c.380dupG | frameshift_variant | 0.89 | 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 | 0.82 |
mshA | 575907 | p.Ala187Val | missense_variant | 0.79 |
ccsA | 620625 | p.Ile245Met | missense_variant | 0.8 |
rpoB | 760315 | p.Val170Ala | missense_variant | 0.78 |
rpoB | 760728 | p.Tyr308Asp | missense_variant | 0.61 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 0.75 |
rpoC | 765463 | p.Asn698Lys | missense_variant | 0.12 |
rpoC | 766645 | p.Glu1092Asp | missense_variant | 0.84 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 0.84 |
mmpL5 | 776182 | p.Asp767Asn | missense_variant | 0.69 |
mmpL5 | 777451 | p.Val344Leu | missense_variant | 0.28 |
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 0.77 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
Rv1258c | 1406760 | c.580_581insC | frameshift_variant | 0.87 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rpsA | 1834177 | c.636A>C | synonymous_variant | 0.79 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
katG | 2154724 | p.Arg463Leu | missense_variant | 0.82 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 0.78 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
ald | 3086742 | c.-78A>C | upstream_gene_variant | 0.24 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 0.77 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243460 | c.228C>T | synonymous_variant | 0.86 |
aftB | 4267647 | p.Asp397Gly | missense_variant | 0.76 |
whiB6 | 4338563 | c.-42G>T | upstream_gene_variant | 0.76 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407588 | c.615A>G | synonymous_variant | 0.83 |
gid | 4407927 | p.Glu92Asp | missense_variant | 0.84 |
gid | 4408213 | c.-11C>T | upstream_gene_variant | 0.26 |