Run ID: ERR212098
Sample name:
Date: 20-10-2023 22:48:34
Number of reads: 6475616
Percentage reads mapped: 99.49
Strain: lineage2.2.1;lineage1.1.2
Drug-resistance: HR-TB
Drug | Resistance | Supporting mutations |
---|---|---|
Rifampicin | ||
Isoniazid | R | katG p.Ser315Thr (0.14) |
Ethambutol | ||
Pyrazinamide | ||
Streptomycin | R | rrs n.513C>T (0.14) |
Fluoroquinolones | ||
Moxifloxacin | ||
Ofloxacin | ||
Levofloxacin | ||
Ciprofloxacin | ||
Aminoglycosides | ||
Amikacin | ||
Capreomycin | ||
Kanamycin | ||
Cycloserine | ||
Ethionamide | ||
Clofazimine | ||
Para-aminosalicylic_acid | ||
Delamanid | ||
Bedaquiline | ||
Linezolid |
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage2 | East-Asian | Beijing | RD105 | 0.83 |
lineage1 | Indo-Oceanic | EAI | RD239 | 0.13 |
lineage1.1 | Indo-Oceanic | EAI3;EAI4;EAI5;EAI6 | RD239 | 0.14 |
lineage2.2 | East-Asian (Beijing) | Beijing-RD207 | RD105;RD207 | 0.86 |
lineage1.1.2 | Indo-Oceanic | EAI3;EAI5 | RD239 | 0.15 |
lineage2.2.1 | East-Asian (Beijing) | Beijing-RD181 | RD105;RD207;RD181 | 0.85 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
rrs | 1472358 | n.513C>T | non_coding_transcript_exon_variant | 0.14 | streptomycin |
katG | 2155168 | p.Ser315Thr | missense_variant | 0.14 | isoniazid |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 6112 | p.Met291Ile | missense_variant | 0.13 |
gyrB | 6124 | c.885C>T | synonymous_variant | 0.15 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 0.99 |
gyrA | 9143 | c.1842T>C | synonymous_variant | 0.16 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 0.99 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 |
mshA | 575907 | p.Ala187Val | missense_variant | 0.83 |
ccsA | 620625 | p.Ile245Met | missense_variant | 0.89 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
rpoC | 763884 | p.Ala172Val | missense_variant | 0.21 |
rpoC | 763886 | c.517C>A | synonymous_variant | 0.21 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 0.99 |
mmpL5 | 776182 | p.Asp767Asn | missense_variant | 0.82 |
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 0.83 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
Rv1258c | 1406760 | c.580_581insC | frameshift_variant | 0.83 |
embR | 1417019 | p.Cys110Tyr | missense_variant | 0.17 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rpsA | 1834177 | c.636A>C | synonymous_variant | 0.86 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
katG | 2154724 | p.Arg463Leu | missense_variant | 0.99 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
PPE35 | 2167983 | p.Gly877Asp | missense_variant | 0.13 |
Rv1979c | 2222308 | p.Asp286Gly | missense_variant | 0.16 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
kasA | 2518132 | c.18C>T | synonymous_variant | 0.14 |
eis | 2714526 | c.805_806delAC | frameshift_variant | 0.76 |
ahpC | 2726051 | c.-142G>A | upstream_gene_variant | 0.13 |
Rv2752c | 3064632 | c.1560C>T | synonymous_variant | 0.17 |
Rv2752c | 3065711 | p.Gly161Ser | missense_variant | 0.87 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
Rv3083 | 3448714 | p.Asp71His | missense_variant | 0.12 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
fprA | 3474597 | c.591C>A | synonymous_variant | 0.15 |
fprA | 3475159 | p.Asn385Asp | missense_variant | 0.19 |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 0.79 |
clpC1 | 4040517 | p.Val63Ala | missense_variant | 0.19 |
embC | 4240671 | p.Thr270Ile | missense_variant | 0.14 |
embC | 4241042 | p.Asn394Asp | missense_variant | 0.16 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243460 | c.228C>T | synonymous_variant | 0.85 |
embA | 4244388 | p.Ala386Thr | missense_variant | 0.84 |
embA | 4245969 | p.Pro913Ser | missense_variant | 0.17 |
embB | 4247646 | p.Glu378Ala | missense_variant | 0.14 |
embB | 4249673 | p.Ser1054Pro | missense_variant | 0.17 |
aftB | 4267647 | p.Asp397Gly | missense_variant | 0.86 |
ubiA | 4269387 | p.Glu149Asp | missense_variant | 0.11 |
aftB | 4269606 | c.-770T>C | upstream_gene_variant | 0.12 |
ethA | 4328209 | c.-736C>A | upstream_gene_variant | 0.14 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
whiB6 | 4338603 | c.-82C>T | upstream_gene_variant | 0.12 |
gid | 4407588 | c.615A>G | synonymous_variant | 0.98 |
gid | 4407873 | c.330G>T | synonymous_variant | 0.17 |
gid | 4407927 | p.Glu92Asp | missense_variant | 0.82 |
gid | 4407935 | p.Leu90Val | missense_variant | 0.15 |
gid | 4407944 | p.Gln87Glu | missense_variant | 0.14 |