Run ID: SRR6045261
Sample name:
Date: 20-10-2023 18:01:00
Number of reads: 1979325
Percentage reads mapped: 91.38
Strain: lineage1.1.2
Drug-resistance: Other
Drug | Resistance | Supporting mutations |
---|---|---|
Rifampicin | ||
Isoniazid | ||
Ethambutol | ||
Pyrazinamide | ||
Streptomycin | R | rrs n.888G>A (0.46) |
Fluoroquinolones | ||
Moxifloxacin | ||
Ofloxacin | ||
Levofloxacin | ||
Ciprofloxacin | ||
Aminoglycosides | ||
Amikacin | ||
Capreomycin | ||
Kanamycin | ||
Cycloserine | ||
Ethionamide | ||
Clofazimine | ||
Para-aminosalicylic_acid | ||
Delamanid | ||
Bedaquiline | ||
Linezolid |
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage1 | Indo-Oceanic | EAI | RD239 | 1.0 |
lineage1.1 | Indo-Oceanic | EAI3;EAI4;EAI5;EAI6 | RD239 | 1.0 |
lineage1.1.2 | Indo-Oceanic | EAI3;EAI5 | RD239 | 1.0 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
rrs | 1472733 | n.888G>A | non_coding_transcript_exon_variant | 0.46 | streptomycin |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 6112 | p.Met291Ile | missense_variant | 1.0 |
gyrB | 6124 | c.885C>T | synonymous_variant | 1.0 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 8366 | c.1065G>C | synonymous_variant | 1.0 |
gyrA | 8452 | p.Ala384Val | missense_variant | 1.0 |
gyrA | 9047 | c.1746C>T | synonymous_variant | 1.0 |
gyrA | 9143 | c.1842T>C | synonymous_variant | 1.0 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
gyrA | 9443 | c.2142G>A | synonymous_variant | 1.0 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 |
mshA | 576000 | p.Asp218Ala | missense_variant | 1.0 |
rpoB | 760490 | c.684C>T | synonymous_variant | 1.0 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
rpoC | 763884 | p.Ala172Val | missense_variant | 1.0 |
rpoC | 763886 | c.517C>A | synonymous_variant | 1.0 |
rpoC | 765171 | p.Pro601Leu | missense_variant | 1.0 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 775979 | c.2502G>A | synonymous_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 |
mmpL5 | 776395 | p.Phe696Leu | missense_variant | 1.0 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
embR | 1417019 | p.Cys110Tyr | missense_variant | 1.0 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1472530 | n.685G>A | non_coding_transcript_exon_variant | 0.45 |
rrs | 1472537 | n.692C>T | non_coding_transcript_exon_variant | 0.45 |
rrs | 1472544 | n.699C>A | non_coding_transcript_exon_variant | 0.45 |
rrs | 1472545 | n.700A>T | non_coding_transcript_exon_variant | 0.45 |
rrs | 1472566 | n.721G>A | non_coding_transcript_exon_variant | 0.47 |
rrs | 1472571 | n.726G>C | non_coding_transcript_exon_variant | 0.45 |
rrs | 1472581 | n.736A>T | non_coding_transcript_exon_variant | 0.62 |
rrs | 1472597 | n.752G>A | non_coding_transcript_exon_variant | 0.25 |
rrs | 1472598 | n.753A>C | non_coding_transcript_exon_variant | 0.42 |
rrs | 1472599 | n.754G>T | non_coding_transcript_exon_variant | 0.42 |
rrs | 1472607 | n.762G>A | non_coding_transcript_exon_variant | 0.24 |
rrs | 1472616 | n.771G>A | non_coding_transcript_exon_variant | 0.52 |
rrs | 1472655 | n.810G>A | non_coding_transcript_exon_variant | 0.71 |
rrs | 1472658 | n.813G>A | non_coding_transcript_exon_variant | 0.59 |
rrs | 1472661 | n.816A>G | non_coding_transcript_exon_variant | 0.55 |
rrs | 1472670 | n.825_830delGGGTTTinsTAGAC | non_coding_transcript_exon_variant | 0.46 |
rrs | 1472680 | n.835C>T | non_coding_transcript_exon_variant | 0.35 |
rrs | 1472689 | n.844C>T | non_coding_transcript_exon_variant | 0.35 |
rrs | 1472690 | n.845C>A | non_coding_transcript_exon_variant | 0.43 |
rrs | 1472697 | n.852T>C | non_coding_transcript_exon_variant | 0.43 |
rrs | 1472713 | n.868T>C | non_coding_transcript_exon_variant | 0.43 |
rrs | 1472716 | n.871C>T | non_coding_transcript_exon_variant | 0.45 |
rrs | 1472742 | n.897C>T | non_coding_transcript_exon_variant | 0.42 |
rrs | 1472744 | n.899A>G | non_coding_transcript_exon_variant | 0.42 |
rrl | 1476225 | n.2568T>G | non_coding_transcript_exon_variant | 0.54 |
rrl | 1476227 | n.2570C>T | non_coding_transcript_exon_variant | 0.58 |
rrl | 1476229 | n.2572C>T | non_coding_transcript_exon_variant | 0.62 |
rrl | 1476250 | n.2593C>G | non_coding_transcript_exon_variant | 0.68 |
rrl | 1476251 | n.2594T>C | non_coding_transcript_exon_variant | 0.68 |
rrl | 1476257 | n.2600G>C | non_coding_transcript_exon_variant | 0.7 |
rrl | 1476260 | n.2603A>G | non_coding_transcript_exon_variant | 0.7 |
rrl | 1476280 | n.2623A>C | non_coding_transcript_exon_variant | 0.67 |
rrl | 1476293 | n.2636C>T | non_coding_transcript_exon_variant | 0.59 |
rrl | 1476294 | n.2637A>G | non_coding_transcript_exon_variant | 0.59 |
rrl | 1476295 | n.2638C>G | non_coding_transcript_exon_variant | 0.59 |
rrl | 1476296 | n.2639C>T | non_coding_transcript_exon_variant | 0.59 |
rrl | 1476297 | n.2640C>T | non_coding_transcript_exon_variant | 0.57 |
rrl | 1476302 | n.2645G>A | non_coding_transcript_exon_variant | 0.52 |
rrl | 1476311 | n.2654G>C | non_coding_transcript_exon_variant | 0.5 |
rrl | 1476312 | n.2655T>C | non_coding_transcript_exon_variant | 0.5 |
rrl | 1476313 | n.2656G>A | non_coding_transcript_exon_variant | 0.5 |
rrl | 1476332 | n.2675G>C | non_coding_transcript_exon_variant | 0.5 |
rrl | 1476338 | n.2681C>T | non_coding_transcript_exon_variant | 0.58 |
rrl | 1476353 | n.2696G>T | non_coding_transcript_exon_variant | 0.7 |
rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.69 |
rrl | 1476369 | n.2712C>T | non_coding_transcript_exon_variant | 0.65 |
rrl | 1476372 | n.2715T>C | non_coding_transcript_exon_variant | 0.67 |
rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.62 |
rrl | 1476383 | n.2726T>A | non_coding_transcript_exon_variant | 0.6 |
rrl | 1476425 | n.2768G>T | non_coding_transcript_exon_variant | 0.64 |
rrl | 1476428 | n.2771C>T | non_coding_transcript_exon_variant | 0.63 |
rrl | 1476429 | n.2772A>C | non_coding_transcript_exon_variant | 0.63 |
rrl | 1476481 | n.2824T>C | non_coding_transcript_exon_variant | 0.65 |
rrl | 1476506 | n.2849T>C | non_coding_transcript_exon_variant | 0.27 |
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 |
PPE35 | 2167983 | p.Gly877Asp | missense_variant | 1.0 |
PPE35 | 2169369 | p.Gly415Ala | missense_variant | 0.98 |
Rv1979c | 2222308 | p.Asp286Gly | missense_variant | 1.0 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
kasA | 2518132 | c.18C>T | synonymous_variant | 1.0 |
ahpC | 2726051 | c.-142G>A | upstream_gene_variant | 1.0 |
Rv2752c | 3064632 | c.1560C>T | synonymous_variant | 1.0 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
Rv3083 | 3448714 | p.Asp71His | missense_variant | 1.0 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
fprA | 3474597 | c.591C>A | synonymous_variant | 1.0 |
fprA | 3475129 | p.Ala375Thr | missense_variant | 0.98 |
fprA | 3475159 | p.Asn385Asp | missense_variant | 1.0 |
clpC1 | 4040517 | p.Val63Ala | missense_variant | 1.0 |
embC | 4240671 | p.Thr270Ile | missense_variant | 1.0 |
embC | 4241042 | p.Asn394Asp | missense_variant | 1.0 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243197 | c.-36C>T | upstream_gene_variant | 1.0 |
embA | 4243848 | p.Val206Met | missense_variant | 1.0 |
embA | 4245969 | p.Pro913Ser | missense_variant | 1.0 |
embB | 4247646 | p.Glu378Ala | missense_variant | 1.0 |
ubiA | 4269387 | p.Glu149Asp | missense_variant | 1.0 |
aftB | 4269606 | c.-770T>C | upstream_gene_variant | 1.0 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
whiB6 | 4338603 | c.-82C>T | upstream_gene_variant | 1.0 |
gid | 4407588 | c.615A>G | synonymous_variant | 1.0 |
gid | 4407873 | c.330G>T | synonymous_variant | 1.0 |