Run ID: ERR2510793
Sample name:
Date: 20-10-2023 06:30:44
Number of reads: 1259481
Percentage reads mapped: 94.8
Strain: lineage4.3.3
Drug-resistance: MDR-TB
Drug | Resistance | Supporting mutations |
---|---|---|
Rifampicin | R | rpoB p.Asp435Val (0.96) |
Isoniazid | R | katG p.Ser315Thr (1.00) |
Ethambutol | R | embB p.Met306Val (1.00) |
Pyrazinamide | R | pncA p.Lys48Thr (1.00) |
Streptomycin | ||
Fluoroquinolones | ||
Moxifloxacin | ||
Ofloxacin | ||
Levofloxacin | ||
Ciprofloxacin | ||
Aminoglycosides | R | rrs n.1401A>G (0.86) |
Amikacin | R | rrs n.1401A>G (0.86) |
Capreomycin | R | rrs n.1401A>G (0.86) |
Kanamycin | R | rrs n.1401A>G (0.86) |
Cycloserine | ||
Ethionamide | R | ethA p.Pro378Leu (1.00) |
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 |
lineage4.3.3 | Euro-American (LAM) | LAM;T | RD115 | 1.0 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
rpoB | 761110 | p.Asp435Val | missense_variant | 0.96 | rifampicin |
rrs | 1473246 | n.1401A>G | non_coding_transcript_exon_variant | 0.86 | kanamycin, capreomycin, aminoglycosides, amikacin |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
pncA | 2289099 | p.Lys48Thr | missense_variant | 1.0 | pyrazinamide |
embB | 4247429 | p.Met306Val | missense_variant | 1.0 | ethambutol |
ethA | 4326341 | p.Pro378Leu | missense_variant | 1.0 | ethionamide |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 8040 | p.Gly247Ser | missense_variant | 1.0 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
mshA | 576516 | p.Val390Ala | missense_variant | 1.0 |
rpoC | 764995 | c.1626C>G | synonymous_variant | 1.0 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1472150 | n.305T>A | non_coding_transcript_exon_variant | 0.25 |
rrs | 1472172 | n.327T>C | non_coding_transcript_exon_variant | 0.18 |
rrs | 1472956 | n.1111T>C | non_coding_transcript_exon_variant | 0.21 |
rrs | 1472957 | n.1112C>T | non_coding_transcript_exon_variant | 0.22 |
rrs | 1472973 | n.1128A>T | non_coding_transcript_exon_variant | 0.24 |
rrs | 1472987 | n.1142G>A | non_coding_transcript_exon_variant | 0.23 |
rrs | 1472990 | n.1145A>G | non_coding_transcript_exon_variant | 0.24 |
rrs | 1473035 | n.1190G>A | non_coding_transcript_exon_variant | 0.38 |
rrs | 1473055 | n.1210C>T | non_coding_transcript_exon_variant | 0.23 |
rrs | 1473056 | n.1211A>T | non_coding_transcript_exon_variant | 0.28 |
rrs | 1473066 | n.1221A>G | non_coding_transcript_exon_variant | 0.24 |
rrs | 1473088 | n.1243A>G | non_coding_transcript_exon_variant | 0.22 |
rrs | 1473093 | n.1248C>T | non_coding_transcript_exon_variant | 0.2 |
rrs | 1473100 | n.1255G>A | non_coding_transcript_exon_variant | 0.2 |
rrs | 1473102 | n.1257C>T | non_coding_transcript_exon_variant | 0.19 |
rrs | 1473104 | n.1259C>T | non_coding_transcript_exon_variant | 0.19 |
rrs | 1473110 | n.1265T>G | non_coding_transcript_exon_variant | 0.19 |
rrs | 1473111 | n.1266A>G | non_coding_transcript_exon_variant | 0.18 |
rrs | 1473121 | n.1276T>C | non_coding_transcript_exon_variant | 0.18 |
rrl | 1476359 | n.2702C>G | non_coding_transcript_exon_variant | 0.14 |
rrl | 1476381 | n.2724G>C | non_coding_transcript_exon_variant | 0.17 |
rrl | 1476428 | n.2771C>T | non_coding_transcript_exon_variant | 0.17 |
rrl | 1476429 | n.2772A>C | non_coding_transcript_exon_variant | 0.15 |
rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.21 |
rrl | 1476481 | n.2824T>C | non_coding_transcript_exon_variant | 0.17 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
kasA | 2518919 | p.Gly269Ser | missense_variant | 1.0 |
thyA | 3073868 | p.Thr202Ala | missense_variant | 1.0 |
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 | 1.0 |
embC | 4242182 | p.Ala774Ser | missense_variant | 1.0 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243392 | p.Asn54Asp | missense_variant | 1.0 |
ubiA | 4269731 | p.Ala35Ser | missense_variant | 1.0 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407986 | p.Gly73Arg | missense_variant | 1.0 |
gid | 4408156 | p.Leu16Arg | missense_variant | 1.0 |