Run ID: ERR4798952
Sample name:
Date: 20-10-2023 03:18:52
Number of reads: 4121144
Percentage reads mapped: 99.47
Strain: lineage4.1.2.1;lineage1.1.2
Drug-resistance: MDR-TB
Drug | Resistance | Supporting mutations |
---|---|---|
Rifampicin | R | rpoB p.Leu430Pro (0.44) |
Isoniazid | R | katG p.Ser315Thr (0.55) |
Ethambutol | R | embB p.Gly406Ser (0.61) |
Pyrazinamide | ||
Streptomycin | R | gid c.102delG (0.41) |
Fluoroquinolones | ||
Moxifloxacin | ||
Ofloxacin | ||
Levofloxacin | ||
Ciprofloxacin | ||
Aminoglycosides | ||
Amikacin | ||
Capreomycin | ||
Kanamycin | ||
Cycloserine | ||
Ethionamide | ||
Clofazimine | ||
Para-aminosalicylic_acid | ||
Delamanid | ||
Bedaquiline | ||
Linezolid |
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage4 | Euro-American | LAM;T;S;X;H | None | 0.52 |
lineage1 | Indo-Oceanic | EAI | RD239 | 0.46 |
lineage4.1 | Euro-American | T;X;H | None | 0.52 |
lineage1.1 | Indo-Oceanic | EAI3;EAI4;EAI5;EAI6 | RD239 | 0.47 |
lineage1.1.2 | Indo-Oceanic | EAI3;EAI5 | RD239 | 0.47 |
lineage4.1.2 | Euro-American | T;H | None | 0.51 |
lineage4.1.2.1 | Euro-American (Haarlem) | T1;H1 | RD182 | 0.51 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
rpoB | 761095 | p.Leu430Pro | missense_variant | 0.44 | rifampicin |
katG | 2155167 | p.Ser315Thr | missense_variant | 0.55 | isoniazid |
embB | 4247729 | p.Gly406Ser | missense_variant | 0.61 | ethambutol |
gid | 4408100 | c.102delG | frameshift_variant | 0.41 | streptomycin |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 6112 | p.Met291Ile | missense_variant | 0.47 |
gyrB | 6124 | c.885C>T | synonymous_variant | 0.52 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 8452 | p.Ala384Val | missense_variant | 0.57 |
gyrA | 9143 | c.1842T>C | synonymous_variant | 0.47 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
fgd1 | 491591 | p.Lys270Met | missense_variant | 0.66 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 0.46 |
mshA | 575679 | p.Asn111Ser | missense_variant | 0.59 |
rpoB | 760115 | c.309C>T | synonymous_variant | 0.64 |
rpoB | 760490 | c.684C>T | synonymous_variant | 0.43 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 0.62 |
rpoC | 763884 | p.Ala172Val | missense_variant | 0.38 |
rpoC | 763886 | c.517C>A | synonymous_variant | 0.38 |
rpoC | 765150 | p.Gly594Glu | missense_variant | 0.57 |
rpoC | 765171 | p.Pro601Leu | missense_variant | 0.4 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 0.54 |
mmpL5 | 776395 | p.Phe696Leu | missense_variant | 0.47 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
embR | 1417019 | p.Cys110Tyr | missense_variant | 0.45 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrl | 1475460 | n.1803A>G | non_coding_transcript_exon_variant | 0.47 |
rpsA | 1833875 | p.Ala112Thr | missense_variant | 0.54 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
katG | 2154724 | p.Arg463Leu | missense_variant | 0.52 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 0.53 |
PPE35 | 2167983 | p.Gly877Asp | missense_variant | 0.52 |
Rv1979c | 2222308 | p.Asp286Gly | missense_variant | 0.33 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
kasA | 2518076 | c.-39C>T | upstream_gene_variant | 0.47 |
kasA | 2518132 | c.18C>T | synonymous_variant | 0.52 |
eis | 2714872 | p.Pro154Leu | missense_variant | 0.45 |
ahpC | 2726051 | c.-142G>A | upstream_gene_variant | 0.44 |
Rv2752c | 3064632 | c.1560C>T | synonymous_variant | 0.46 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 0.99 |
Rv3083 | 3448714 | p.Asp71His | missense_variant | 0.43 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
fprA | 3474597 | c.591C>A | synonymous_variant | 0.51 |
fprA | 3475159 | p.Asn385Asp | missense_variant | 0.44 |
whiB7 | 3568759 | c.-80A>C | upstream_gene_variant | 0.5 |
clpC1 | 4040517 | p.Val63Ala | missense_variant | 0.41 |
embC | 4240671 | p.Thr270Ile | missense_variant | 0.48 |
embC | 4241042 | p.Asn394Asp | missense_variant | 0.44 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embC | 4242803 | p.Val981Leu | missense_variant | 0.59 |
embA | 4243848 | p.Val206Met | missense_variant | 0.4 |
embA | 4245218 | c.1986C>T | synonymous_variant | 0.52 |
embA | 4245969 | p.Pro913Ser | missense_variant | 0.46 |
embB | 4247646 | p.Glu378Ala | missense_variant | 0.39 |
ubiA | 4269031 | p.Gly268Asp | missense_variant | 0.5 |
ubiA | 4269387 | p.Glu149Asp | missense_variant | 0.52 |
aftB | 4269606 | c.-770T>C | upstream_gene_variant | 0.5 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
whiB6 | 4338603 | c.-82C>T | upstream_gene_variant | 0.54 |
gid | 4407588 | c.615A>G | synonymous_variant | 0.53 |
gid | 4407873 | c.330G>T | synonymous_variant | 0.54 |