Run ID: SRR6650323
Sample name:
Date: 15-08-2023 07:37:35
Number of reads: 1675171
Percentage reads mapped: 99.32
Strain: lineage1.2.2.2
Drug-resistance: Other
Drug | Resistance | Supporting mutations |
---|---|---|
Rifampicin | ||
Isoniazid | ||
Ethambutol | ||
Pyrazinamide | ||
Streptomycin | R | gid c.115delC (1.00) |
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 |
lineage1.2.2 | Indo-Oceanic | EAI1 | RD239 | 1.0 |
lineage1.2.2.2 | Indo-Oceanic | NA | RD239 | 1.0 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
gid | 4408087 | c.115delC | frameshift_variant | 1.0 | streptomycin |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 5075 | c.-165C>T | upstream_gene_variant | 1.0 |
gyrB | 5530 | c.291C>T | synonymous_variant | 1.0 |
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 | 491742 | c.960T>C | synonymous_variant | 1.0 |
mshA | 576723 | p.Val459Gly | missense_variant | 0.22 |
ccsA | 620770 | p.Trp294Arg | missense_variant | 0.14 |
ccsA | 620773 | p.Ile295Val | missense_variant | 0.19 |
rpoB | 759620 | c.-187A>C | upstream_gene_variant | 0.25 |
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 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 |
mmpR5 | 779371 | p.Ala128Pro | missense_variant | 0.2 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
rplC | 801287 | p.Val160Gly | missense_variant | 0.28 |
rplC | 801302 | p.Arg165Pro | missense_variant | 0.18 |
fbiC | 1303016 | p.Val29Gly | missense_variant | 0.19 |
embR | 1417019 | p.Cys110Tyr | missense_variant | 1.0 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrl | 1473916 | n.259C>A | non_coding_transcript_exon_variant | 0.25 |
rrl | 1474469 | n.812T>G | non_coding_transcript_exon_variant | 0.2 |
rrl | 1474489 | n.832T>G | non_coding_transcript_exon_variant | 0.33 |
rrl | 1474500 | n.843T>G | non_coding_transcript_exon_variant | 0.33 |
rrl | 1476170 | n.2513C>A | non_coding_transcript_exon_variant | 0.22 |
fabG1 | 1673690 | p.Val84Gly | missense_variant | 0.22 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
tlyA | 1918052 | p.Pro38Arg | missense_variant | 0.18 |
ndh | 2103225 | c.-183A>C | upstream_gene_variant | 0.27 |
ndh | 2103235 | c.-193C>G | upstream_gene_variant | 0.15 |
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
PPE35 | 2168742 | p.Gly624Asp | missense_variant | 0.95 |
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 | 2714566 | p.Leu256Pro | missense_variant | 0.17 |
ahpC | 2726051 | c.-142G>A | upstream_gene_variant | 1.0 |
Rv2752c | 3064889 | p.Lys435Glu | missense_variant | 1.0 |
thyA | 3074430 | c.42G>A | synonymous_variant | 1.0 |
thyA | 3074641 | c.-170C>T | upstream_gene_variant | 0.17 |
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 |
fbiB | 3642772 | p.Asp413Ala | missense_variant | 0.24 |
alr | 3841506 | c.-86A>C | upstream_gene_variant | 0.22 |
alr | 3841546 | c.-126C>A | upstream_gene_variant | 1.0 |
clpC1 | 4040517 | p.Val63Ala | missense_variant | 1.0 |
embC | 4239973 | c.111T>G | synonymous_variant | 0.17 |
embC | 4240671 | p.Thr270Ile | missense_variant | 1.0 |
embC | 4241042 | p.Asn394Asp | missense_variant | 1.0 |
embC | 4241809 | c.1947A>G | synonymous_variant | 1.0 |
embC | 4242220 | c.2358A>C | synonymous_variant | 0.35 |
embA | 4242406 | c.-827A>C | upstream_gene_variant | 0.23 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4245969 | p.Pro913Ser | missense_variant | 1.0 |
embB | 4247646 | p.Glu378Ala | missense_variant | 1.0 |
embB | 4249322 | p.Ala937Lys | missense_variant | 0.2 |
aftB | 4268245 | p.Ile198Val | missense_variant | 0.21 |
aftB | 4268776 | p.Ser21Gly | missense_variant | 0.25 |
aftB | 4268786 | c.51C>T | synonymous_variant | 0.18 |
ubiA | 4269387 | p.Glu149Asp | missense_variant | 1.0 |
ubiA | 4269502 | p.Val111Gly | missense_variant | 0.28 |
aftB | 4269504 | c.-668A>G | upstream_gene_variant | 0.34 |
ubiA | 4269511 | p.Val108Gly | missense_variant | 0.29 |
aftB | 4269606 | c.-770T>C | upstream_gene_variant | 1.0 |
ethA | 4326439 | p.Asn345Lys | missense_variant | 1.0 |
ethR | 4326898 | c.-651C>G | upstream_gene_variant | 0.17 |
ethA | 4326905 | p.Leu190Pro | missense_variant | 0.15 |
ethA | 4328193 | c.-720G>A | upstream_gene_variant | 1.0 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
whiB6 | 4338603 | c.-82C>T | upstream_gene_variant | 1.0 |
whiB6 | 4338635 | c.-114A>C | upstream_gene_variant | 1.0 |
gid | 4407588 | c.615A>G | synonymous_variant | 1.0 |
gid | 4407873 | c.330G>T | synonymous_variant | 1.0 |