Run ID: ERR4819414
Sample name:
Date: 20-10-2023 08:56:58
Number of reads: 4625554
Percentage reads mapped: 95.75
Strain: lineage1.1.3.1
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 |
lineage1.1.3 | Indo-Oceanic | EAI6 | RD239 | 1.0 |
lineage1.1.3.1 | Indo-Oceanic | NA | RD239 | 1.0 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|
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 | 9304 | p.Gly668Asp | missense_variant | 1.0 |
fgd1 | 491521 | p.Arg247Trp | missense_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 | 1.0 |
rpoC | 763886 | c.517C>A | synonymous_variant | 1.0 |
rpoC | 764647 | c.1278C>T | synonymous_variant | 0.12 |
rpoC | 764653 | c.1284G>C | synonymous_variant | 0.12 |
rpoC | 764662 | c.1293G>C | synonymous_variant | 0.11 |
rpoC | 764677 | c.1308C>G | synonymous_variant | 0.1 |
rpoC | 764678 | p.Lys437Gln | missense_variant | 0.1 |
rpoC | 764692 | c.1323C>T | synonymous_variant | 0.12 |
rpoC | 765171 | p.Pro601Leu | missense_variant | 1.0 |
rpoC | 765230 | p.Ala621Thr | missense_variant | 1.0 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 |
mmpS5 | 779526 | c.-621G>A | upstream_gene_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 | 1472150 | n.305T>A | non_coding_transcript_exon_variant | 0.41 |
rrs | 1472155 | n.310C>T | non_coding_transcript_exon_variant | 0.29 |
rrs | 1472160 | n.315C>T | non_coding_transcript_exon_variant | 0.29 |
rrs | 1472225 | n.380C>G | non_coding_transcript_exon_variant | 0.33 |
rrs | 1472251 | n.406G>A | non_coding_transcript_exon_variant | 0.59 |
rrs | 1472259 | n.414C>A | non_coding_transcript_exon_variant | 0.4 |
rrs | 1472571 | n.726G>C | non_coding_transcript_exon_variant | 0.43 |
rrs | 1472581 | n.736A>C | non_coding_transcript_exon_variant | 0.33 |
rrs | 1472581 | n.736A>T | non_coding_transcript_exon_variant | 0.46 |
rrs | 1472584 | n.739A>T | non_coding_transcript_exon_variant | 0.33 |
rrs | 1472598 | n.753A>C | non_coding_transcript_exon_variant | 0.45 |
rrs | 1472599 | n.754G>T | non_coding_transcript_exon_variant | 0.45 |
rrs | 1472616 | n.771G>A | non_coding_transcript_exon_variant | 0.32 |
rrs | 1472790 | n.945T>C | non_coding_transcript_exon_variant | 0.52 |
rrs | 1472824 | n.979T>A | non_coding_transcript_exon_variant | 0.54 |
rrs | 1472954 | n.1109T>C | non_coding_transcript_exon_variant | 0.43 |
rrs | 1472956 | n.1111T>C | non_coding_transcript_exon_variant | 0.62 |
rrs | 1472957 | n.1112C>T | non_coding_transcript_exon_variant | 0.48 |
rrs | 1472973 | n.1128A>G | non_coding_transcript_exon_variant | 0.6 |
rrs | 1472990 | n.1145A>G | non_coding_transcript_exon_variant | 0.68 |
rrs | 1472992 | n.1147A>G | non_coding_transcript_exon_variant | 0.47 |
rrs | 1473005 | n.1160C>T | non_coding_transcript_exon_variant | 0.53 |
rrs | 1473035 | n.1190G>A | non_coding_transcript_exon_variant | 0.68 |
rrs | 1473055 | n.1210C>T | non_coding_transcript_exon_variant | 0.71 |
rrs | 1473056 | n.1211A>T | non_coding_transcript_exon_variant | 0.71 |
rrs | 1473066 | n.1221A>G | non_coding_transcript_exon_variant | 0.69 |
rrs | 1473080 | n.1235C>T | non_coding_transcript_exon_variant | 0.41 |
rrs | 1473081 | n.1236C>T | non_coding_transcript_exon_variant | 0.45 |
rrs | 1473088 | n.1243A>G | non_coding_transcript_exon_variant | 0.57 |
rrs | 1473093 | n.1248C>T | non_coding_transcript_exon_variant | 0.52 |
rrs | 1473100 | n.1255G>A | non_coding_transcript_exon_variant | 0.5 |
rrs | 1473121 | n.1276T>C | non_coding_transcript_exon_variant | 0.45 |
rrs | 1473123 | n.1278A>T | non_coding_transcript_exon_variant | 0.43 |
rrs | 1473130 | n.1285G>A | non_coding_transcript_exon_variant | 0.4 |
rrs | 1473145 | n.1300C>T | non_coding_transcript_exon_variant | 0.55 |
rrs | 1473166 | n.1321G>A | non_coding_transcript_exon_variant | 0.51 |
rrs | 1473172 | n.1327T>G | non_coding_transcript_exon_variant | 0.42 |
rrs | 1473173 | n.1328C>T | non_coding_transcript_exon_variant | 0.44 |
rrs | 1473221 | n.1376C>T | non_coding_transcript_exon_variant | 0.36 |
rrs | 1473252 | n.1407T>C | non_coding_transcript_exon_variant | 0.32 |
rrl | 1476381 | n.2724G>C | non_coding_transcript_exon_variant | 0.59 |
rrl | 1476428 | n.2771C>T | non_coding_transcript_exon_variant | 0.57 |
rrl | 1476429 | n.2772A>T | non_coding_transcript_exon_variant | 0.5 |
rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.4 |
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 |
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 | 3475159 | p.Asn385Asp | missense_variant | 1.0 |
alr | 3841253 | c.168C>T | synonymous_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 | 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 |
gid | 4407588 | c.615A>G | synonymous_variant | 1.0 |
gid | 4407780 | c.423G>A | synonymous_variant | 1.0 |
gid | 4407873 | c.330G>T | synonymous_variant | 1.0 |
whiB6 | 4338429 | c.-218_92del | frameshift_variant&start_lost | 1.0 |