Run ID: ERR11067627
Sample name:
Date: 05-04-2023 02:52:05
Number of reads: 3380839
Percentage reads mapped: 99.54
Strain: lineage2.2.1
Drug-resistance: 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 |
rpsL | 781687 | p.Lys43Arg | missense_variant | 1.0 | streptomycin |
rplC | 801268 | p.Cys154Arg | missense_variant | 1.0 | linezolid |
rrs | 1473246 | n.1401A>G | non_coding_transcript_exon_variant | 0.99 | kanamycin, capreomycin, aminoglycosides, amikacin |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
pncA | 2288848 | p.Gly132Ser | missense_variant | 1.0 | pyrazinamide |
embB | 4247431 | p.Met306Ile | missense_variant | 1.0 | ethambutol |
ethA | 4324386 | c.-95_*1617del | transcript_ablation | 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 |
mshA | 576108 | p.Ala254Gly | missense_variant | 0.29 |
mshA | 576456 | p.Val370Gly | missense_variant | 0.55 |
mshA | 576483 | p.Val379Gly | missense_variant | 0.4 |
mshA | 576606 | p.Ala420Gly | missense_variant | 0.27 |
mshA | 576613 | c.1266A>C | synonymous_variant | 0.73 |
mshA | 576616 | c.1269G>C | synonymous_variant | 0.25 |
ccsA | 620625 | p.Ile245Met | missense_variant | 1.0 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
rpoC | 764367 | p.Gly333Ala | missense_variant | 0.2 |
rpoC | 764817 | p.Val483Gly | 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 | 777883 | p.Gly200Arg | missense_variant | 0.4 |
mmpR5 | 779130 | c.144dupC | frameshift_variant | 1.0 |
mmpR5 | 779311 | p.Ile108Val | 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 | 1303157 | p.His76Pro | missense_variant | 0.3 |
Rv1258c | 1406760 | c.580_581insC | frameshift_variant | 1.0 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrl | 1476058 | n.2401T>G | non_coding_transcript_exon_variant | 0.25 |
rpsA | 1834177 | c.636A>C | synonymous_variant | 1.0 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
tlyA | 1918621 | p.Ser228Arg | missense_variant | 0.22 |
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
PPE35 | 2170035 | p.Val193Gly | missense_variant | 0.31 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
kasA | 2519071 | p.Asp319Glu | missense_variant | 0.3 |
thyX | 3067958 | c.-13T>G | upstream_gene_variant | 0.16 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
ald | 3087012 | c.196dupG | frameshift_variant | 1.0 |
fbiD | 3339734 | p.Ala206Gly | missense_variant | 0.71 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 1.0 |
rpoA | 3878580 | c.-73A>C | upstream_gene_variant | 0.29 |
rpoA | 3878641 | c.-134C>G | upstream_gene_variant | 0.89 |
clpC1 | 4040550 | p.Leu52Trp | missense_variant | 0.19 |
embC | 4240409 | p.Pro183Ala | missense_variant | 0.18 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243460 | c.228C>T | synonymous_variant | 1.0 |
embA | 4243682 | c.450T>G | synonymous_variant | 0.22 |
embB | 4246527 | p.Ala5Gly | missense_variant | 0.59 |
embB | 4247016 | p.Ser168Trp | missense_variant | 0.42 |
embB | 4247020 | c.507C>G | synonymous_variant | 0.8 |
embB | 4247028 | p.Leu172Arg | missense_variant | 0.5 |
embB | 4247033 | p.Ser174Arg | missense_variant | 0.43 |
embB | 4248328 | c.1815G>C | synonymous_variant | 0.16 |
aftB | 4267400 | c.1437G>C | synonymous_variant | 0.28 |
aftB | 4267647 | p.Asp397Gly | missense_variant | 1.0 |
whiB6 | 4338200 | p.Asp108His | missense_variant | 0.23 |
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 |