Run ID: ERR4815680
Sample name:
Date: 20-10-2023 07:53:58
Number of reads: 1366619
Percentage reads mapped: 97.06
Strain: lineage1.1.2
Drug-resistance: Other
Drug | Resistance | Supporting mutations |
---|---|---|
Rifampicin | ||
Isoniazid | ||
Ethambutol | ||
Pyrazinamide | ||
Streptomycin | R | rrs n.888G>A (0.37) |
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 | 0.37 | 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 | 0.97 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 0.98 |
gyrA | 8452 | p.Ala384Val | missense_variant | 1.0 |
gyrA | 8542 | p.Val414Ala | missense_variant | 1.0 |
gyrA | 9143 | c.1842T>C | synonymous_variant | 1.0 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 |
rpoB | 760490 | c.684C>T | synonymous_variant | 1.0 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 0.97 |
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 | 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 | 1472106 | n.261G>A | non_coding_transcript_exon_variant | 0.31 |
rrs | 1472108 | n.263C>T | non_coding_transcript_exon_variant | 0.21 |
rrs | 1472150 | n.305T>A | non_coding_transcript_exon_variant | 0.38 |
rrs | 1472172 | n.327T>C | non_coding_transcript_exon_variant | 0.3 |
rrs | 1472410 | n.565A>G | non_coding_transcript_exon_variant | 1.0 |
rrs | 1472581 | n.736A>T | non_coding_transcript_exon_variant | 0.55 |
rrs | 1472655 | n.810G>A | non_coding_transcript_exon_variant | 0.5 |
rrs | 1473035 | n.1190G>A | non_coding_transcript_exon_variant | 0.47 |
rrs | 1473055 | n.1210C>T | non_coding_transcript_exon_variant | 0.34 |
rrs | 1473056 | n.1211A>T | non_coding_transcript_exon_variant | 0.38 |
rrs | 1473066 | n.1221A>G | non_coding_transcript_exon_variant | 0.34 |
rrs | 1473088 | n.1243A>G | non_coding_transcript_exon_variant | 0.38 |
rrs | 1473093 | n.1248C>T | non_coding_transcript_exon_variant | 0.57 |
rrs | 1473100 | n.1255G>A | non_coding_transcript_exon_variant | 0.55 |
rrs | 1473102 | n.1257C>T | non_coding_transcript_exon_variant | 0.55 |
rrs | 1473104 | n.1259C>T | non_coding_transcript_exon_variant | 0.55 |
rrs | 1473110 | n.1265T>G | non_coding_transcript_exon_variant | 0.55 |
rrs | 1473111 | n.1266A>G | non_coding_transcript_exon_variant | 0.41 |
rrs | 1473115 | n.1270G>T | non_coding_transcript_exon_variant | 0.45 |
rrs | 1473121 | n.1276T>C | non_coding_transcript_exon_variant | 0.57 |
rrs | 1473145 | n.1300C>T | non_coding_transcript_exon_variant | 0.53 |
rrs | 1473166 | n.1321G>A | non_coding_transcript_exon_variant | 0.4 |
rrl | 1476381 | n.2724G>C | non_coding_transcript_exon_variant | 0.27 |
rrl | 1476428 | n.2771C>T | non_coding_transcript_exon_variant | 0.29 |
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 |
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 |
eis | 2715016 | p.Arg106His | missense_variant | 1.0 |
ahpC | 2726051 | c.-142G>A | upstream_gene_variant | 1.0 |
pepQ | 2860398 | c.21A>C | synonymous_variant | 1.0 |
Rv2752c | 3064632 | c.1560C>T | synonymous_variant | 1.0 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 0.97 |
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 | 3475159 | p.Asn385Asp | missense_variant | 1.0 |
clpC1 | 4040517 | p.Val63Ala | missense_variant | 0.98 |
embC | 4240671 | p.Thr270Ile | missense_variant | 1.0 |
embC | 4241042 | p.Asn394Asp | missense_variant | 1.0 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 0.98 |
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 | 0.97 |