Run ID: ERR4819119
Sample name:
Date: 20-10-2023 08:51:49
Number of reads: 1767530
Percentage reads mapped: 91.14
Strain: lineage1.2.1.2.1
Drug-resistance: HR-TB
Drug | Resistance | Supporting mutations |
---|---|---|
Rifampicin | ||
Isoniazid | R | fabG1 c.-15C>T (1.00), katG p.Thr380Ile (1.00) |
Ethambutol | ||
Pyrazinamide | ||
Streptomycin | R | rrs n.888G>A (0.21), gid c.102delG (1.00) |
Fluoroquinolones | ||
Moxifloxacin | ||
Ofloxacin | ||
Levofloxacin | ||
Ciprofloxacin | ||
Aminoglycosides | ||
Amikacin | ||
Capreomycin | ||
Kanamycin | ||
Cycloserine | ||
Ethionamide | R | fabG1 c.-15C>T (1.00) |
Clofazimine | ||
Para-aminosalicylic_acid | ||
Delamanid | ||
Bedaquiline | ||
Linezolid |
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage1 | Indo-Oceanic | EAI | RD239 | 1.0 |
lineage1.2.1 | Indo-Oceanic | EAI2 | RD239 | 1.0 |
lineage1.2.1.2 | Indo-Oceanic | NA | RD239 | 1.0 |
lineage1.2.1.2.1 | Indo-Oceanic | NA | RD239 | 1.0 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
rrs | 1472733 | n.888G>A | non_coding_transcript_exon_variant | 0.21 | streptomycin |
fabG1 | 1673425 | c.-15C>T | upstream_gene_variant | 1.0 | isoniazid, ethionamide |
katG | 2154973 | p.Thr380Ile | missense_variant | 1.0 | isoniazid |
gid | 4408100 | c.102delG | frameshift_variant | 1.0 | streptomycin |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 6112 | p.Met291Ile | missense_variant | 1.0 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 8452 | p.Ala384Val | missense_variant | 1.0 |
gyrA | 9143 | c.1842T>C | synonymous_variant | 1.0 |
gyrA | 9260 | c.1959G>C | synonymous_variant | 1.0 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 |
mshA | 575368 | c.21T>C | synonymous_variant | 1.0 |
rpoC | 762902 | c.-468C>T | upstream_gene_variant | 0.17 |
rpoC | 762911 | c.-459C>T | upstream_gene_variant | 0.24 |
rpoC | 762917 | c.-453C>T | upstream_gene_variant | 0.24 |
rpoC | 762920 | c.-450C>T | upstream_gene_variant | 0.24 |
rpoC | 762929 | c.-441G>T | upstream_gene_variant | 0.27 |
rpoC | 762944 | c.-426C>T | upstream_gene_variant | 0.34 |
rpoC | 762956 | c.-414G>T | upstream_gene_variant | 0.35 |
rpoC | 762962 | c.-408C>T | upstream_gene_variant | 0.32 |
rpoC | 762983 | c.-387C>T | upstream_gene_variant | 0.34 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
rpoC | 763531 | c.162G>C | synonymous_variant | 1.0 |
rpoC | 763884 | p.Ala172Val | missense_variant | 1.0 |
rpoC | 763886 | c.517C>A | synonymous_variant | 1.0 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
Rv1258c | 1406312 | c.1029T>C | synonymous_variant | 1.0 |
embR | 1417019 | p.Cys110Tyr | missense_variant | 1.0 |
atpE | 1460907 | c.-138T>C | upstream_gene_variant | 1.0 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1472112 | n.267C>T | non_coding_transcript_exon_variant | 0.64 |
rrs | 1472113 | n.268T>C | non_coding_transcript_exon_variant | 0.67 |
rrs | 1472150 | n.305T>A | non_coding_transcript_exon_variant | 0.96 |
rrs | 1472155 | n.310C>T | non_coding_transcript_exon_variant | 0.18 |
rrs | 1472172 | n.327T>C | non_coding_transcript_exon_variant | 0.81 |
rrs | 1472251 | n.406G>A | non_coding_transcript_exon_variant | 0.96 |
rrs | 1472537 | n.692C>T | non_coding_transcript_exon_variant | 0.93 |
rrs | 1472544 | n.699C>A | non_coding_transcript_exon_variant | 0.93 |
rrs | 1472545 | n.700A>T | non_coding_transcript_exon_variant | 0.93 |
rrs | 1472566 | n.721G>A | non_coding_transcript_exon_variant | 0.89 |
rrs | 1472571 | n.726G>C | non_coding_transcript_exon_variant | 0.85 |
rrs | 1472579 | n.734G>T | non_coding_transcript_exon_variant | 0.82 |
rrs | 1472581 | n.736A>T | non_coding_transcript_exon_variant | 0.89 |
rrs | 1472598 | n.753A>C | non_coding_transcript_exon_variant | 0.81 |
rrs | 1472599 | n.754G>T | non_coding_transcript_exon_variant | 0.81 |
rrs | 1472616 | n.771G>A | non_coding_transcript_exon_variant | 0.38 |
rrs | 1472714 | n.869A>G | non_coding_transcript_exon_variant | 0.82 |
rrs | 1472742 | n.897C>T | non_coding_transcript_exon_variant | 0.19 |
rrs | 1472744 | n.899A>G | non_coding_transcript_exon_variant | 0.19 |
rrs | 1472755 | n.910G>A | non_coding_transcript_exon_variant | 0.73 |
rrs | 1472781 | n.936C>T | non_coding_transcript_exon_variant | 0.17 |
rrs | 1472790 | n.945T>C | non_coding_transcript_exon_variant | 0.76 |
rrs | 1472793 | n.948A>T | non_coding_transcript_exon_variant | 0.19 |
rrs | 1472803 | n.958T>A | non_coding_transcript_exon_variant | 0.2 |
rrs | 1472895 | n.1050C>T | non_coding_transcript_exon_variant | 1.0 |
rrs | 1472952 | n.1107T>C | non_coding_transcript_exon_variant | 0.77 |
rrs | 1472955 | n.1110C>T | non_coding_transcript_exon_variant | 0.83 |
rrs | 1472956 | n.1111T>C | non_coding_transcript_exon_variant | 1.0 |
rrs | 1472957 | n.1112C>T | non_coding_transcript_exon_variant | 0.97 |
rrs | 1472973 | n.1128A>T | non_coding_transcript_exon_variant | 0.26 |
rrs | 1472987 | n.1142G>A | non_coding_transcript_exon_variant | 0.9 |
rrs | 1472989 | n.1144G>A | non_coding_transcript_exon_variant | 0.9 |
rrs | 1472990 | n.1145A>G | non_coding_transcript_exon_variant | 1.0 |
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 | 1.0 |
rrs | 1473088 | n.1243A>G | non_coding_transcript_exon_variant | 1.0 |
rrs | 1473093 | n.1248C>T | non_coding_transcript_exon_variant | 0.95 |
rrs | 1473100 | n.1255G>A | non_coding_transcript_exon_variant | 1.0 |
rrs | 1473102 | n.1257C>T | non_coding_transcript_exon_variant | 1.0 |
rrs | 1473104 | n.1259C>T | non_coding_transcript_exon_variant | 1.0 |
rrs | 1473110 | n.1265T>G | non_coding_transcript_exon_variant | 1.0 |
rrs | 1473111 | n.1266A>G | non_coding_transcript_exon_variant | 1.0 |
rrs | 1473115 | n.1270G>T | non_coding_transcript_exon_variant | 0.96 |
rrs | 1473121 | n.1276T>C | non_coding_transcript_exon_variant | 0.94 |
rrs | 1473145 | n.1300C>T | non_coding_transcript_exon_variant | 0.95 |
rrs | 1473166 | n.1321G>A | non_coding_transcript_exon_variant | 0.95 |
rrs | 1473172 | n.1327T>G | non_coding_transcript_exon_variant | 0.18 |
rrs | 1473173 | n.1328C>T | non_coding_transcript_exon_variant | 0.23 |
rrl | 1474249 | n.592G>T | non_coding_transcript_exon_variant | 0.71 |
rrl | 1476250 | n.2593C>G | non_coding_transcript_exon_variant | 0.73 |
rrl | 1476251 | n.2594T>C | non_coding_transcript_exon_variant | 0.73 |
rrl | 1476257 | n.2600G>C | non_coding_transcript_exon_variant | 0.62 |
rrl | 1476260 | n.2603A>G | non_coding_transcript_exon_variant | 0.62 |
rrl | 1476359 | n.2702C>G | non_coding_transcript_exon_variant | 0.87 |
rrl | 1476381 | n.2724G>C | non_coding_transcript_exon_variant | 0.93 |
rrl | 1476428 | n.2771C>T | non_coding_transcript_exon_variant | 0.88 |
rrl | 1476429 | n.2772A>C | non_coding_transcript_exon_variant | 0.88 |
rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.95 |
inhA | 1674162 | c.-40C>T | upstream_gene_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 | 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 |
kasA | 2519048 | p.Gly312Ser | missense_variant | 1.0 |
ahpC | 2726051 | c.-142G>A | upstream_gene_variant | 1.0 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
fbiD | 3339417 | c.300A>G | synonymous_variant | 1.0 |
Rv3083 | 3448714 | p.Asp71His | missense_variant | 1.0 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
fprA | 3474579 | c.573C>T | synonymous_variant | 1.0 |
fprA | 3474597 | c.591C>A | synonymous_variant | 1.0 |
fprA | 3475159 | p.Asn385Asp | missense_variant | 1.0 |
whiB7 | 3568488 | c.191delG | frameshift_variant | 1.0 |
fbiB | 3640557 | c.-978T>C | upstream_gene_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 | 4243580 | c.348G>A | synonymous_variant | 1.0 |
embA | 4244420 | c.1188G>C | synonymous_variant | 1.0 |
embA | 4245969 | p.Pro913Ser | missense_variant | 1.0 |
embB | 4247578 | c.1065G>A | synonymous_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 |
ubiA | 4269864 | c.-32delG | upstream_gene_variant | 1.0 |
whiB6 | 4338361 | p.Arg54Gln | missense_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 |