Run ID: SRR6824519
Sample name:
Date: 20-10-2023 19:43:04
Number of reads: 18207455
Percentage reads mapped: 97.97
Strain: lineage2.2.1
Drug-resistance: MDR-TB
Drug | Resistance | Supporting mutations |
---|---|---|
Rifampicin | R | rpoB p.Ser450Leu (1.00) |
Isoniazid | R | katG p.Ser315Thr (1.00) |
Ethambutol | ||
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 | 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 |
---|---|---|---|---|---|
rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin |
rpsL | 781687 | p.Lys43Arg | missense_variant | 1.0 | streptomycin |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 5086 | c.-154A>C | upstream_gene_variant | 1.0 |
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 |
rpoB | 762653 | p.Trp949Cys | missense_variant | 1.0 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
rpoC | 764660 | p.Val431Met | 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 | 777745 | p.Gly246Ser | missense_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 |
rrs | 1472598 | n.753A>C | non_coding_transcript_exon_variant | 0.11 |
rrs | 1472616 | n.771G>A | non_coding_transcript_exon_variant | 0.19 |
rrs | 1472655 | n.810G>A | non_coding_transcript_exon_variant | 0.18 |
rrs | 1472658 | n.813G>A | non_coding_transcript_exon_variant | 0.17 |
rrs | 1472661 | n.816A>G | non_coding_transcript_exon_variant | 0.16 |
rrs | 1472665 | n.820G>A | non_coding_transcript_exon_variant | 0.15 |
rrs | 1472669 | n.824_825insTAGA | non_coding_transcript_exon_variant | 0.15 |
rrs | 1472678 | n.833T>G | non_coding_transcript_exon_variant | 0.15 |
rrs | 1472679 | n.834T>C | non_coding_transcript_exon_variant | 0.15 |
rrs | 1472682 | n.839_843delGGGAT | non_coding_transcript_exon_variant | 0.15 |
rrs | 1472689 | n.844C>T | non_coding_transcript_exon_variant | 0.15 |
rrs | 1472690 | n.845C>A | non_coding_transcript_exon_variant | 0.15 |
rrs | 1472695 | n.850C>T | non_coding_transcript_exon_variant | 0.15 |
rrs | 1472697 | n.852T>C | non_coding_transcript_exon_variant | 0.15 |
rrs | 1472701 | n.856T>A | non_coding_transcript_exon_variant | 0.16 |
rrs | 1472713 | n.868T>C | non_coding_transcript_exon_variant | 0.17 |
rrs | 1472716 | n.871C>T | non_coding_transcript_exon_variant | 0.17 |
rrs | 1472744 | n.899A>G | non_coding_transcript_exon_variant | 0.15 |
rrl | 1476153 | n.2496T>C | non_coding_transcript_exon_variant | 0.12 |
rrl | 1476165 | n.2508T>A | non_coding_transcript_exon_variant | 0.12 |
rrl | 1476194 | n.2537A>G | non_coding_transcript_exon_variant | 0.12 |
rrl | 1476195 | n.2538C>A | non_coding_transcript_exon_variant | 0.12 |
rrl | 1476196 | n.2539C>A | non_coding_transcript_exon_variant | 0.12 |
rrl | 1476200 | n.2543A>T | non_coding_transcript_exon_variant | 0.12 |
rrl | 1476201 | n.2544C>T | non_coding_transcript_exon_variant | 0.13 |
rrl | 1476204 | n.2547C>A | non_coding_transcript_exon_variant | 0.13 |
rrl | 1476210 | n.2553G>T | non_coding_transcript_exon_variant | 0.12 |
rrl | 1476211 | n.2554G>T | non_coding_transcript_exon_variant | 0.13 |
rrl | 1476212 | n.2555T>C | non_coding_transcript_exon_variant | 0.13 |
rrl | 1476214 | n.2557G>T | non_coding_transcript_exon_variant | 0.13 |
rrl | 1476215 | n.2558C>A | non_coding_transcript_exon_variant | 0.13 |
rrl | 1476225 | n.2568T>G | non_coding_transcript_exon_variant | 0.17 |
rrl | 1476251 | n.2594T>C | non_coding_transcript_exon_variant | 0.26 |
rrl | 1476260 | n.2603A>G | non_coding_transcript_exon_variant | 0.28 |
rrl | 1476280 | n.2623A>C | non_coding_transcript_exon_variant | 0.28 |
rrl | 1476293 | n.2636C>T | non_coding_transcript_exon_variant | 0.23 |
rrl | 1476294 | n.2637A>G | non_coding_transcript_exon_variant | 0.23 |
rrl | 1476295 | n.2638C>G | non_coding_transcript_exon_variant | 0.23 |
rrl | 1476296 | n.2639C>T | non_coding_transcript_exon_variant | 0.23 |
rrl | 1476297 | n.2640C>T | non_coding_transcript_exon_variant | 0.23 |
rrl | 1476301 | n.2644A>C | non_coding_transcript_exon_variant | 0.23 |
rrl | 1476302 | n.2645G>A | non_coding_transcript_exon_variant | 0.23 |
rrl | 1476311 | n.2654G>C | non_coding_transcript_exon_variant | 0.23 |
rrl | 1476312 | n.2655T>C | non_coding_transcript_exon_variant | 0.24 |
rrl | 1476313 | n.2656G>A | non_coding_transcript_exon_variant | 0.24 |
rrl | 1476332 | n.2675G>C | non_coding_transcript_exon_variant | 0.31 |
rrl | 1476353 | n.2696G>T | non_coding_transcript_exon_variant | 0.34 |
rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.38 |
rrl | 1476372 | n.2715T>C | non_coding_transcript_exon_variant | 0.37 |
rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.33 |
rrl | 1476383 | n.2726T>A | non_coding_transcript_exon_variant | 0.34 |
rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.3 |
rrl | 1476425 | n.2768G>T | non_coding_transcript_exon_variant | 0.26 |
rrl | 1476428 | n.2771C>T | non_coding_transcript_exon_variant | 0.25 |
rrl | 1476429 | n.2772A>C | non_coding_transcript_exon_variant | 0.26 |
rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.27 |
rrl | 1476481 | n.2824T>C | non_coding_transcript_exon_variant | 0.23 |
rrl | 1476506 | n.2849T>C | non_coding_transcript_exon_variant | 0.14 |
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 |
embA | 4244087 | c.855G>A | synonymous_variant | 1.0 |
aftB | 4267647 | p.Asp397Gly | missense_variant | 1.0 |
ethA | 4326993 | p.Ile161Val | missense_variant | 0.99 |
whiB6 | 4338412 | p.Asp37Gly | 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 |