Run ID: ERR775800
Sample name:
Date: 19-10-2023 08:49:04
Number of reads: 5999066
Percentage reads mapped: 92.2
Strain: lineage1.1
Drug-resistance: Sensitive
Drug | Resistance | Supporting mutations |
---|---|---|
Rifampicin | ||
Isoniazid | ||
Ethambutol | ||
Pyrazinamide | ||
Streptomycin | ||
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 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 6112 | p.Met291Ile | missense_variant | 0.99 |
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 | 9304 | p.Gly668Asp | missense_variant | 1.0 |
gyrA | 9491 | c.2190C>T | synonymous_variant | 1.0 |
gyrA | 9527 | c.2226A>C | synonymous_variant | 1.0 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
rpoC | 763884 | p.Ala172Val | missense_variant | 0.99 |
rpoC | 763886 | c.517C>A | synonymous_variant | 0.99 |
rpoC | 765171 | p.Pro601Leu | missense_variant | 1.0 |
rpoC | 766009 | c.2640G>C | synonymous_variant | 1.0 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776041 | p.Ala814Thr | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
embR | 1416230 | p.Asp373Gly | missense_variant | 1.0 |
embR | 1417019 | p.Cys110Tyr | missense_variant | 1.0 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1472127 | n.282C>T | non_coding_transcript_exon_variant | 0.13 |
rrs | 1472129 | n.284G>C | non_coding_transcript_exon_variant | 0.12 |
rrs | 1472137 | n.292G>A | non_coding_transcript_exon_variant | 0.12 |
rrs | 1472150 | n.305T>A | non_coding_transcript_exon_variant | 0.12 |
rrs | 1472151 | n.306C>A | non_coding_transcript_exon_variant | 0.13 |
rrs | 1472172 | n.327T>C | non_coding_transcript_exon_variant | 0.15 |
rrs | 1472557 | n.712G>A | non_coding_transcript_exon_variant | 0.25 |
rrs | 1472570 | n.725G>A | non_coding_transcript_exon_variant | 0.23 |
rrs | 1472571 | n.726G>C | non_coding_transcript_exon_variant | 0.24 |
rrs | 1472581 | n.736A>T | non_coding_transcript_exon_variant | 0.23 |
rrs | 1472598 | n.753A>C | non_coding_transcript_exon_variant | 0.19 |
rrs | 1472616 | n.771G>A | non_coding_transcript_exon_variant | 0.12 |
rrs | 1472744 | n.899A>G | non_coding_transcript_exon_variant | 0.19 |
rrs | 1472767 | n.922G>A | non_coding_transcript_exon_variant | 0.19 |
rrs | 1472779 | n.934G>A | non_coding_transcript_exon_variant | 0.17 |
rrs | 1472781 | n.936C>T | non_coding_transcript_exon_variant | 0.18 |
rrs | 1472786 | n.941C>T | non_coding_transcript_exon_variant | 0.19 |
rrs | 1472793 | n.948A>T | non_coding_transcript_exon_variant | 0.19 |
rrs | 1472803 | n.958T>A | non_coding_transcript_exon_variant | 0.18 |
rrs | 1473002 | n.1157G>T | non_coding_transcript_exon_variant | 0.13 |
rrs | 1473004 | n.1159T>A | non_coding_transcript_exon_variant | 0.13 |
rrs | 1473008 | n.1163C>A | non_coding_transcript_exon_variant | 0.13 |
rrs | 1473009 | n.1164T>C | non_coding_transcript_exon_variant | 0.13 |
rrs | 1473161 | n.1316A>C | non_coding_transcript_exon_variant | 0.11 |
rrs | 1473164 | n.1319C>G | non_coding_transcript_exon_variant | 0.11 |
rrs | 1473177 | n.1332G>A | non_coding_transcript_exon_variant | 0.12 |
rrs | 1473192 | n.1347A>G | non_coding_transcript_exon_variant | 0.1 |
rrs | 1473205 | n.1360T>C | non_coding_transcript_exon_variant | 0.1 |
rrl | 1474798 | n.1141C>T | non_coding_transcript_exon_variant | 0.2 |
rrl | 1474804 | n.1147C>T | non_coding_transcript_exon_variant | 0.23 |
rrl | 1474823 | n.1166C>G | non_coding_transcript_exon_variant | 0.26 |
rrl | 1474827 | n.1170C>T | non_coding_transcript_exon_variant | 0.29 |
rrl | 1474831 | n.1174A>C | non_coding_transcript_exon_variant | 0.33 |
rrl | 1474844 | n.1187G>T | non_coding_transcript_exon_variant | 0.36 |
rrl | 1474866 | n.1209C>A | non_coding_transcript_exon_variant | 0.34 |
rrl | 1474869 | n.1212G>T | non_coding_transcript_exon_variant | 0.32 |
rrl | 1474896 | n.1239A>G | non_coding_transcript_exon_variant | 0.29 |
rrl | 1474902 | n.1245T>C | non_coding_transcript_exon_variant | 0.24 |
rrl | 1474904 | n.1247G>C | non_coding_transcript_exon_variant | 0.25 |
rrl | 1474913 | n.1256T>A | non_coding_transcript_exon_variant | 0.2 |
rrl | 1474920 | n.1263G>A | non_coding_transcript_exon_variant | 0.19 |
rrl | 1476332 | n.2675G>C | non_coding_transcript_exon_variant | 0.14 |
rrl | 1476338 | n.2681C>T | non_coding_transcript_exon_variant | 0.16 |
rrl | 1476353 | n.2696G>T | non_coding_transcript_exon_variant | 0.27 |
rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.3 |
rrl | 1476372 | n.2715T>C | non_coding_transcript_exon_variant | 0.38 |
rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.38 |
rrl | 1476383 | n.2726T>A | non_coding_transcript_exon_variant | 0.38 |
rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.46 |
rrl | 1476425 | n.2768G>A | non_coding_transcript_exon_variant | 0.46 |
rrl | 1476428 | n.2771C>T | non_coding_transcript_exon_variant | 0.47 |
rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.33 |
rrl | 1476481 | n.2824T>C | non_coding_transcript_exon_variant | 0.24 |
rrl | 1476506 | n.2849T>C | non_coding_transcript_exon_variant | 0.13 |
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 | 0.99 |
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 | 2725990 | c.-203T>C | upstream_gene_variant | 1.0 |
ahpC | 2726051 | c.-142G>A | upstream_gene_variant | 1.0 |
folC | 2747757 | c.-159G>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 |
fbiD | 3339101 | c.-17G>A | upstream_gene_variant | 1.0 |
Rv3083 | 3448606 | c.103C>T | synonymous_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 | 3475159 | p.Asn385Asp | missense_variant | 1.0 |
Rv3236c | 3612739 | c.378C>T | synonymous_variant | 0.99 |
alr | 3840636 | p.Pro262Leu | missense_variant | 1.0 |
alr | 3841399 | p.Val8Ile | 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 | 4243848 | p.Val206Met | missense_variant | 1.0 |
embA | 4244695 | p.Lys488Met | missense_variant | 0.99 |
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 | 4407680 | p.Arg175Trp | missense_variant | 1.0 |
gid | 4407873 | c.330G>T | synonymous_variant | 1.0 |