Run ID: ERR4818698
Sample name:
Date: 20-10-2023 08:44:46
Number of reads: 1835016
Percentage reads mapped: 92.55
Strain: lineage2.2.1
Drug-resistance: HR-TB
Drug | Resistance | Supporting mutations |
---|---|---|
Rifampicin | ||
Isoniazid | R | katG p.Ser315Thr (1.00) |
Ethambutol | R | embB p.Met306Val (1.00) |
Pyrazinamide | ||
Streptomycin | R | rpsL p.Lys43Arg (1.00), rrs n.888G>A (0.65) |
Fluoroquinolones | ||
Moxifloxacin | ||
Ofloxacin | ||
Levofloxacin | ||
Ciprofloxacin | ||
Aminoglycosides | ||
Amikacin | ||
Capreomycin | ||
Kanamycin | ||
Cycloserine | ||
Ethionamide | ||
Clofazimine | ||
Para-aminosalicylic_acid | ||
Delamanid | ||
Bedaquiline | ||
Linezolid |
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 |
---|---|---|---|---|---|
rpsL | 781687 | p.Lys43Arg | missense_variant | 1.0 | streptomycin |
rrs | 1472733 | n.888G>A | non_coding_transcript_exon_variant | 0.65 | streptomycin |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
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 |
ccsA | 620625 | p.Ile245Met | missense_variant | 1.0 |
rpoC | 763031 | c.-339T>C | upstream_gene_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 |
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 1.0 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
fbiC | 1304644 | p.Gly572Cys | missense_variant | 1.0 |
Rv1258c | 1406760 | c.580_581insC | frameshift_variant | 1.0 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1472108 | n.263C>T | non_coding_transcript_exon_variant | 0.79 |
rrs | 1472122 | n.277G>T | non_coding_transcript_exon_variant | 0.75 |
rrs | 1472123 | n.278A>T | non_coding_transcript_exon_variant | 0.79 |
rrs | 1472124 | n.279C>T | non_coding_transcript_exon_variant | 0.75 |
rrs | 1472150 | n.305T>A | non_coding_transcript_exon_variant | 0.88 |
rrs | 1472155 | n.310C>T | non_coding_transcript_exon_variant | 0.6 |
rrs | 1472160 | n.315C>T | non_coding_transcript_exon_variant | 0.7 |
rrs | 1472251 | n.406G>A | non_coding_transcript_exon_variant | 0.92 |
rrs | 1472537 | n.692C>T | non_coding_transcript_exon_variant | 0.83 |
rrs | 1472544 | n.699C>A | non_coding_transcript_exon_variant | 0.88 |
rrs | 1472545 | n.700A>T | non_coding_transcript_exon_variant | 0.88 |
rrs | 1472566 | n.721G>A | non_coding_transcript_exon_variant | 0.91 |
rrs | 1472571 | n.726G>C | non_coding_transcript_exon_variant | 0.91 |
rrs | 1472579 | n.734G>T | non_coding_transcript_exon_variant | 0.87 |
rrs | 1472581 | n.736A>T | non_coding_transcript_exon_variant | 1.0 |
rrs | 1472598 | n.753A>C | non_coding_transcript_exon_variant | 0.9 |
rrs | 1472599 | n.754G>T | non_coding_transcript_exon_variant | 0.9 |
rrs | 1472616 | n.771G>A | non_coding_transcript_exon_variant | 0.3 |
rrs | 1472714 | n.869A>G | non_coding_transcript_exon_variant | 0.36 |
rrs | 1472742 | n.897C>T | non_coding_transcript_exon_variant | 0.61 |
rrs | 1472744 | n.899A>G | non_coding_transcript_exon_variant | 0.61 |
rrs | 1472781 | n.936C>T | non_coding_transcript_exon_variant | 0.62 |
rrs | 1472790 | n.945T>C | non_coding_transcript_exon_variant | 0.35 |
rrs | 1472793 | n.948A>T | non_coding_transcript_exon_variant | 0.6 |
rrs | 1472803 | n.958T>A | non_coding_transcript_exon_variant | 0.57 |
rrs | 1472895 | n.1050C>T | non_coding_transcript_exon_variant | 0.76 |
rrs | 1472954 | n.1109T>C | non_coding_transcript_exon_variant | 0.43 |
rrs | 1472956 | n.1111T>C | non_coding_transcript_exon_variant | 0.67 |
rrs | 1472957 | n.1112C>T | non_coding_transcript_exon_variant | 0.86 |
rrs | 1472973 | n.1128A>G | non_coding_transcript_exon_variant | 0.46 |
rrs | 1472990 | n.1145A>G | non_coding_transcript_exon_variant | 0.95 |
rrs | 1472992 | n.1147A>G | non_coding_transcript_exon_variant | 0.42 |
rrs | 1473005 | n.1160C>T | non_coding_transcript_exon_variant | 0.52 |
rrs | 1473035 | n.1190G>A | non_coding_transcript_exon_variant | 1.0 |
rrs | 1473055 | n.1210C>T | non_coding_transcript_exon_variant | 1.0 |
rrs | 1473056 | n.1211A>T | non_coding_transcript_exon_variant | 1.0 |
rrs | 1473066 | n.1221A>G | non_coding_transcript_exon_variant | 0.97 |
rrs | 1473080 | n.1235C>T | non_coding_transcript_exon_variant | 0.61 |
rrs | 1473088 | n.1243A>G | non_coding_transcript_exon_variant | 0.95 |
rrs | 1473145 | n.1300C>T | non_coding_transcript_exon_variant | 0.93 |
rrs | 1473166 | n.1321G>A | non_coding_transcript_exon_variant | 0.94 |
rrs | 1473172 | n.1327T>G | non_coding_transcript_exon_variant | 0.61 |
rrs | 1473173 | n.1328C>T | non_coding_transcript_exon_variant | 0.61 |
rrs | 1473221 | n.1376C>T | non_coding_transcript_exon_variant | 0.51 |
rrs | 1473252 | n.1407T>C | non_coding_transcript_exon_variant | 0.68 |
rrs | 1473259 | n.1414C>T | non_coding_transcript_exon_variant | 0.8 |
rrs | 1473276 | n.1431A>C | non_coding_transcript_exon_variant | 0.67 |
rrl | 1476381 | n.2724G>C | non_coding_transcript_exon_variant | 0.74 |
rrl | 1476428 | n.2771C>T | non_coding_transcript_exon_variant | 0.73 |
rrl | 1476429 | n.2772A>C | non_coding_transcript_exon_variant | 0.28 |
rrl | 1476429 | n.2772A>T | non_coding_transcript_exon_variant | 0.44 |
rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.75 |
rrl | 1476481 | n.2824T>C | non_coding_transcript_exon_variant | 0.56 |
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 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
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 | 1.0 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243460 | c.228C>T | synonymous_variant | 1.0 |
aftB | 4267647 | p.Asp397Gly | missense_variant | 1.0 |
ethA | 4327065 | p.Cys137Arg | missense_variant | 1.0 |
whiB6 | 4338487 | p.Cys12Ser | missense_variant | 1.0 |
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 |