Run ID: ERR1213930
Sample name:
Date: 19-10-2023 21:02:45
Number of reads: 4865630
Percentage reads mapped: 92.47
Strain: lineage4.3.2
Drug-resistance: Other
Drug | Resistance | Supporting mutations |
---|---|---|
Rifampicin | ||
Isoniazid | ||
Ethambutol | ||
Pyrazinamide | ||
Streptomycin | R | rrs n.462C>T (0.34) |
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 | 1.0 |
lineage4.3 | Euro-American (LAM) | mainly-LAM | None | 1.0 |
lineage4.3.2 | Euro-American (LAM) | LAM3 | None | 0.99 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
rrs | 1472307 | n.462C>T | non_coding_transcript_exon_variant | 0.34 | streptomycin |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 8619 | c.1318T>C | synonymous_variant | 0.12 |
gyrA | 8627 | c.1326C>G | synonymous_variant | 0.13 |
gyrA | 8636 | c.1335A>C | synonymous_variant | 0.13 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
rpoB | 761636 | c.1830G>C | synonymous_variant | 0.12 |
rpoC | 764995 | c.1626C>G | synonymous_variant | 0.89 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776230 | c.2251T>C | synonymous_variant | 0.14 |
mmpL5 | 776234 | c.2247A>G | synonymous_variant | 0.12 |
mmpL5 | 777455 | c.1026G>C | synonymous_variant | 0.14 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1471969 | n.124T>C | non_coding_transcript_exon_variant | 0.33 |
rrs | 1472300 | n.455C>T | non_coding_transcript_exon_variant | 0.35 |
rrs | 1472337 | n.492C>T | non_coding_transcript_exon_variant | 0.55 |
rrs | 1473123 | n.1278A>T | non_coding_transcript_exon_variant | 0.3 |
rrs | 1473290 | n.1445delCinsTT | non_coding_transcript_exon_variant | 0.3 |
rrl | 1473752 | n.95G>T | non_coding_transcript_exon_variant | 0.3 |
rrl | 1473806 | n.149C>T | non_coding_transcript_exon_variant | 0.46 |
rrl | 1473815 | n.158T>C | non_coding_transcript_exon_variant | 0.48 |
rrl | 1473836 | n.179A>G | non_coding_transcript_exon_variant | 0.6 |
rrl | 1473876 | n.219G>A | non_coding_transcript_exon_variant | 0.29 |
rrl | 1473877 | n.220G>A | non_coding_transcript_exon_variant | 0.29 |
rrl | 1473898 | n.241C>T | non_coding_transcript_exon_variant | 0.29 |
rrl | 1473943 | n.286G>T | non_coding_transcript_exon_variant | 0.29 |
rrl | 1473944 | n.287G>T | non_coding_transcript_exon_variant | 0.29 |
rrl | 1474001 | n.344C>T | non_coding_transcript_exon_variant | 0.2 |
rrl | 1474028 | n.371T>C | non_coding_transcript_exon_variant | 0.21 |
rrl | 1474029 | n.372G>A | non_coding_transcript_exon_variant | 0.21 |
rrl | 1474034 | n.377G>A | non_coding_transcript_exon_variant | 0.22 |
rrl | 1474111 | n.454T>C | non_coding_transcript_exon_variant | 0.35 |
rrl | 1474140 | n.483C>T | non_coding_transcript_exon_variant | 0.45 |
rrl | 1474151 | n.494C>T | non_coding_transcript_exon_variant | 0.55 |
rrl | 1474181 | n.524C>A | non_coding_transcript_exon_variant | 0.48 |
rrl | 1474266 | n.609T>C | non_coding_transcript_exon_variant | 0.41 |
rrl | 1474794 | n.1137C>A | non_coding_transcript_exon_variant | 0.32 |
rrl | 1475202 | n.1545G>C | non_coding_transcript_exon_variant | 0.26 |
rrl | 1475213 | n.1556C>T | non_coding_transcript_exon_variant | 0.33 |
rrl | 1475252 | n.1595C>T | non_coding_transcript_exon_variant | 0.32 |
rrl | 1475266 | n.1609T>C | non_coding_transcript_exon_variant | 0.34 |
rrl | 1475276 | n.1619T>C | non_coding_transcript_exon_variant | 0.36 |
rrl | 1475505 | n.1848G>A | non_coding_transcript_exon_variant | 0.35 |
rrl | 1475526 | n.1869C>A | non_coding_transcript_exon_variant | 0.23 |
rrl | 1475608 | n.1951T>C | non_coding_transcript_exon_variant | 0.21 |
rrl | 1475638 | n.1981C>T | non_coding_transcript_exon_variant | 0.31 |
rrl | 1475657 | n.2000A>G | non_coding_transcript_exon_variant | 0.33 |
rrl | 1475881 | n.2224T>C | non_coding_transcript_exon_variant | 0.18 |
rrl | 1475988 | n.2331A>G | non_coding_transcript_exon_variant | 0.21 |
rrl | 1475997 | n.2340A>T | non_coding_transcript_exon_variant | 0.21 |
rrl | 1476056 | n.2399G>A | non_coding_transcript_exon_variant | 0.21 |
rrl | 1476086 | n.2429G>A | non_coding_transcript_exon_variant | 0.21 |
rrl | 1476214 | n.2557G>A | non_coding_transcript_exon_variant | 0.19 |
rrl | 1476224 | n.2567A>G | non_coding_transcript_exon_variant | 0.18 |
rrl | 1476281 | n.2624T>C | non_coding_transcript_exon_variant | 0.39 |
rrl | 1476297 | n.2640C>T | non_coding_transcript_exon_variant | 0.5 |
rrl | 1476299 | n.2642C>T | non_coding_transcript_exon_variant | 0.5 |
rrl | 1476583 | n.2926G>A | non_coding_transcript_exon_variant | 0.38 |
rrl | 1476597 | n.2940G>A | non_coding_transcript_exon_variant | 0.34 |
rrl | 1476628 | n.2971T>A | non_coding_transcript_exon_variant | 0.3 |
rrl | 1476629 | n.2972C>A | non_coding_transcript_exon_variant | 0.3 |
rrl | 1476716 | n.3059A>C | non_coding_transcript_exon_variant | 0.47 |
rrl | 1476726 | n.3069A>G | non_coding_transcript_exon_variant | 0.46 |
rrl | 1476746 | n.3089T>A | non_coding_transcript_exon_variant | 0.31 |
rrl | 1476755 | n.3098G>T | non_coding_transcript_exon_variant | 0.22 |
rrl | 1476759 | n.3102T>A | non_coding_transcript_exon_variant | 0.19 |
fabG1 | 1674037 | p.Gln200Glu | missense_variant | 0.17 |
inhA | 1674051 | c.-151A>G | upstream_gene_variant | 0.15 |
inhA | 1674054 | c.-148T>C | upstream_gene_variant | 0.13 |
inhA | 1674060 | c.-142A>G | upstream_gene_variant | 0.16 |
inhA | 1674063 | c.-139G>C | upstream_gene_variant | 0.16 |
fabG1 | 1674079 | p.Pro214Ala | missense_variant | 0.19 |
inhA | 1674570 | c.369G>C | synonymous_variant | 0.14 |
inhA | 1674589 | p.Met130Leu | missense_variant | 0.18 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
thyA | 3073868 | p.Thr202Ala | missense_variant | 0.97 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
clpC1 | 4038287 | c.2418C>T | synonymous_variant | 0.97 |
clpC1 | 4039064 | c.1641C>A | synonymous_variant | 0.21 |
clpC1 | 4039079 | c.1626C>G | synonymous_variant | 0.21 |
clpC1 | 4039928 | c.775_777delAGCinsTCG | synonymous_variant | 0.13 |
clpC1 | 4039937 | c.768G>C | synonymous_variant | 0.12 |
clpC1 | 4039946 | c.759A>C | synonymous_variant | 0.13 |
clpC1 | 4040063 | c.642G>C | synonymous_variant | 0.12 |
embC | 4240853 | c.991C>T | synonymous_variant | 0.13 |
embC | 4242498 | p.Arg879Lys | missense_variant | 0.94 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
aftB | 4269372 | c.-536G>A | upstream_gene_variant | 0.14 |
ubiA | 4269380 | p.Val152Ile | missense_variant | 0.13 |
ubiA | 4269387 | p.Glu149Asp | missense_variant | 0.13 |
aftB | 4269390 | c.-554G>C | upstream_gene_variant | 0.12 |
aftB | 4269402 | c.-566T>C | upstream_gene_variant | 0.14 |
aftB | 4269411 | c.-575T>C | upstream_gene_variant | 0.13 |
aftB | 4269414 | c.-578T>C | upstream_gene_variant | 0.13 |
aftB | 4269420 | c.-584T>C | upstream_gene_variant | 0.12 |
ubiA | 4269424 | p.Ala137Gly | missense_variant | 0.13 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4408156 | p.Leu16Arg | missense_variant | 1.0 |