Run ID: ERR1035318
Sample name:
Date: 20-10-2023 21:39:36
Number of reads: 7286199
Percentage reads mapped: 98.72
Strain: lineage4.3.4.1
Drug-resistance: Pre-XDR-TB
| Drug | Resistance | Supporting mutations |
|---|---|---|
| Rifampicin | R | rpoB p.Ser450Leu (0.99) |
| Isoniazid | R | fabG1 c.-15C>T (1.00), inhA p.Ile194Thr (0.97) |
| Ethambutol | R | embA c.-12C>T (1.00), embB p.Gln497Arg (0.98) |
| Pyrazinamide | R | pncA p.Asp63His (1.00) |
| Streptomycin | R | rpsL p.Lys43Arg (0.98) |
| Fluoroquinolones | R | gyrA p.Asp94Gly (0.99) |
| Moxifloxacin | R | gyrA p.Asp94Gly (0.99) |
| Ofloxacin | R | gyrA p.Asp94Gly (0.99) |
| Levofloxacin | R | gyrA p.Asp94Gly (0.99) |
| Ciprofloxacin | R | gyrA p.Asp94Gly (0.99) |
| Aminoglycosides | ||
| Amikacin | ||
| Capreomycin | ||
| Kanamycin | ||
| Cycloserine | R | ald c.992dupC (0.86) |
| Ethionamide | R | fabG1 c.-15C>T (1.00), inhA p.Ile194Thr (0.97) |
| Clofazimine | ||
| Para-aminosalicylic_acid | R | thyX c.-16C>T (1.00) |
| 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 |
| lineage4.3.4 | Euro-American (LAM) | LAM | RD174 | 1.0 |
| lineage4.3.4.1 | Euro-American (LAM) | LAM1;LAM2 | RD174 | 1.0 |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
|---|---|---|---|---|---|
| gyrA | 7582 | p.Asp94Gly | missense_variant | 0.99 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
| rpoB | 761155 | p.Ser450Leu | missense_variant | 0.99 | rifampicin |
| rpsL | 781687 | p.Lys43Arg | missense_variant | 0.98 | streptomycin |
| fabG1 | 1673425 | c.-15C>T | upstream_gene_variant | 1.0 | isoniazid, ethionamide |
| inhA | 1674782 | p.Ile194Thr | missense_variant | 0.97 | isoniazid, ethionamide |
| pncA | 2289055 | p.Asp63His | missense_variant | 1.0 | pyrazinamide |
| thyX | 3067961 | c.-16C>T | upstream_gene_variant | 1.0 | para-aminosalicylic_acid |
| ald | 3087810 | c.992dupC | frameshift_variant | 0.86 | cycloserine |
| embA | 4243221 | c.-12C>T | upstream_gene_variant | 1.0 | ethambutol |
| embB | 4248003 | p.Gln497Arg | missense_variant | 0.98 | ethambutol |
| Gene | Chromosome position | Mutation | Type | Estimated fraction |
|---|---|---|---|---|
| gyrB | 6028 | c.789C>T | synonymous_variant | 1.0 |
| gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
| gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
| gyrA | 8639 | c.1338G>A | synonymous_variant | 1.0 |
| gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
| rpoB | 759608 | c.-199C>T | upstream_gene_variant | 1.0 |
| rpoB | 761998 | p.Leu731Pro | missense_variant | 0.99 |
| rpoC | 764995 | c.1626C>G | synonymous_variant | 0.99 |
| mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
| rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
| rplC | 801066 | c.258G>A | synonymous_variant | 1.0 |
| rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
| rrl | 1473752 | n.95G>T | non_coding_transcript_exon_variant | 0.15 |
| rrl | 1473806 | n.149C>T | non_coding_transcript_exon_variant | 0.16 |
| rrl | 1473815 | n.158T>C | non_coding_transcript_exon_variant | 0.25 |
| rrl | 1473836 | n.179A>G | non_coding_transcript_exon_variant | 0.28 |
| rrl | 1474140 | n.483C>T | non_coding_transcript_exon_variant | 0.23 |
| rrl | 1474151 | n.494C>T | non_coding_transcript_exon_variant | 0.21 |
| rrl | 1474181 | n.524C>A | non_coding_transcript_exon_variant | 0.3 |
| rrl | 1474266 | n.609T>C | non_coding_transcript_exon_variant | 0.21 |
| rrl | 1474716 | n.1059A>G | non_coding_transcript_exon_variant | 0.2 |
| rrl | 1474831 | n.1174A>G | non_coding_transcript_exon_variant | 0.23 |
| tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
| katG | 2155721 | p.Pro131Ser | missense_variant | 0.99 |
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
| ahpC | 2726323 | p.Pro44Arg | missense_variant | 1.0 |
| thyA | 3073868 | p.Thr202Ala | missense_variant | 0.99 |
| ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
| Rv3083 | 3448598 | p.Ile32Thr | missense_variant | 1.0 |
| fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
| Rv3236c | 3612009 | p.Ala370Thr | missense_variant | 1.0 |
| rpoA | 3878270 | p.Leu80Val | missense_variant | 1.0 |
| clpC1 | 4038287 | c.2418C>T | synonymous_variant | 1.0 |
| embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
| aftB | 4268982 | c.-146G>A | upstream_gene_variant | 1.0 |
| whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
| gid | 4408156 | p.Leu16Arg | missense_variant | 1.0 |
