Run ID: ERR019572
Sample name:
Date: 20-10-2023 23:27:36
Number of reads: 4137677
Percentage reads mapped: 92.51
Strain: lineage2.2.1
Drug-resistance: HR-TB
Drug | Resistance | Supporting mutations |
---|---|---|
Rifampicin | ||
Isoniazid | R | katG p.Ser315Thr (0.97) |
Ethambutol | R | embA c.-12C>T (1.00), embB p.Met306Val (1.00) |
Pyrazinamide | ||
Streptomycin | R | rpsL p.Lys43Arg (1.00) |
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 | 0.99 |
lineage2.2 | East-Asian (Beijing) | Beijing-RD207 | RD105;RD207 | 0.99 |
lineage2.2.1 | East-Asian (Beijing) | Beijing-RD181 | RD105;RD207;RD181 | 0.98 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
rpsL | 781687 | p.Lys43Arg | missense_variant | 1.0 | streptomycin |
katG | 2155168 | p.Ser315Thr | missense_variant | 0.97 | isoniazid |
embA | 4243221 | c.-12C>T | upstream_gene_variant | 1.0 | ethambutol |
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 | 0.98 |
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 | 0.97 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 |
mmpL5 | 776182 | p.Asp767Asn | missense_variant | 0.96 |
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 | 0.97 |
rrs | 1472172 | n.327T>C | non_coding_transcript_exon_variant | 0.18 |
rrs | 1472378 | n.533G>T | non_coding_transcript_exon_variant | 0.11 |
rrs | 1472379 | n.534T>G | non_coding_transcript_exon_variant | 0.1 |
rrs | 1472382 | n.537G>A | non_coding_transcript_exon_variant | 0.1 |
rrs | 1472598 | n.753A>C | non_coding_transcript_exon_variant | 0.41 |
rrs | 1472616 | n.771G>A | non_coding_transcript_exon_variant | 0.41 |
rrs | 1472713 | n.868T>C | non_coding_transcript_exon_variant | 0.18 |
rrs | 1472716 | n.871C>T | non_coding_transcript_exon_variant | 0.21 |
rrs | 1472744 | n.899A>G | non_coding_transcript_exon_variant | 0.45 |
rrs | 1472781 | n.936C>T | non_coding_transcript_exon_variant | 0.51 |
rrs | 1472793 | n.948A>T | non_coding_transcript_exon_variant | 0.36 |
rrs | 1472803 | n.958T>A | non_coding_transcript_exon_variant | 0.28 |
rrs | 1472895 | n.1050C>T | non_coding_transcript_exon_variant | 0.34 |
rrs | 1473035 | n.1190G>A | non_coding_transcript_exon_variant | 0.31 |
rrs | 1473053 | n.1208T>A | non_coding_transcript_exon_variant | 0.34 |
rrs | 1473056 | n.1211A>T | non_coding_transcript_exon_variant | 0.32 |
rrs | 1473062 | n.1217T>A | non_coding_transcript_exon_variant | 0.29 |
rrs | 1473068 | n.1223A>G | non_coding_transcript_exon_variant | 0.23 |
rrs | 1473192 | n.1347A>G | non_coding_transcript_exon_variant | 0.17 |
rrs | 1473201 | n.1356_1357delACinsT | non_coding_transcript_exon_variant | 0.21 |
rrs | 1473205 | n.1360T>C | non_coding_transcript_exon_variant | 0.17 |
rrl | 1475816 | n.2159C>G | non_coding_transcript_exon_variant | 0.19 |
rrl | 1475817 | n.2160A>G | non_coding_transcript_exon_variant | 0.19 |
rrl | 1475858 | n.2201T>C | non_coding_transcript_exon_variant | 0.19 |
rrl | 1476251 | n.2594T>C | non_coding_transcript_exon_variant | 0.28 |
rrl | 1476260 | n.2603A>G | non_coding_transcript_exon_variant | 0.27 |
rrl | 1476280 | n.2623A>C | non_coding_transcript_exon_variant | 0.25 |
rrl | 1476332 | n.2675G>C | non_coding_transcript_exon_variant | 0.38 |
rrl | 1476353 | n.2696G>T | non_coding_transcript_exon_variant | 0.48 |
rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.52 |
rrl | 1476372 | n.2715T>C | non_coding_transcript_exon_variant | 0.5 |
rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.48 |
rrl | 1476383 | n.2726T>A | non_coding_transcript_exon_variant | 0.48 |
rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.63 |
rrl | 1476425 | n.2768G>T | non_coding_transcript_exon_variant | 0.53 |
rrl | 1476428 | n.2771C>T | non_coding_transcript_exon_variant | 0.57 |
rrl | 1476429 | n.2772A>C | non_coding_transcript_exon_variant | 0.57 |
rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.46 |
rrl | 1476481 | n.2824T>C | non_coding_transcript_exon_variant | 0.37 |
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 | 2222112 | c.1052dupT | frameshift_variant | 0.98 |
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 |
ddn | 3986931 | p.Arg30Ser | 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 |
ethR | 4327870 | p.Asn108Asp | 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 |