Run ID: SRR8651637
Sample name:
Date: 21-10-2023 13:02:46
Number of reads: 10923698
Percentage reads mapped: 99.57
Strain: lineage4.4.2
Drug-resistance: Pre-XDR-TB
| Drug | Resistance | Supporting mutations |
|---|---|---|
| Rifampicin | R | rpoB p.Leu430Pro (0.99), rpoB p.Asp435Asn (0.98) |
| Isoniazid | R | katG p.Ser315Thr (1.00) |
| Ethambutol | R | embB p.Gln497Pro (0.99) |
| Pyrazinamide | R | pncA p.Thr47Pro (1.00) |
| Streptomycin | R | rrs n.514A>C (1.00) |
| Fluoroquinolones | R | gyrB p.Ala504Val (0.87), gyrA p.Ala90Val (0.98) |
| Moxifloxacin | R | gyrB p.Ala504Val (0.87), gyrA p.Ala90Val (0.98) |
| Ofloxacin | R | gyrB p.Ala504Val (0.87), gyrA p.Ala90Val (0.98) |
| Levofloxacin | R | gyrB p.Ala504Val (0.87), gyrA p.Ala90Val (0.98) |
| Ciprofloxacin | R | gyrB p.Ala504Val (0.87), gyrA p.Ala90Val (0.98) |
| 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 |
| lineage4.4 | Euro-American | S;T | None | 1.0 |
| lineage4.4.2 | Euro-American | T1;T2 | None | 1.0 |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
|---|---|---|---|---|---|
| gyrB | 6750 | p.Ala504Val | missense_variant | 0.87 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
| gyrA | 7570 | p.Ala90Val | missense_variant | 0.98 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
| rpoB | 761095 | p.Leu430Pro | missense_variant | 0.99 | rifampicin |
| rpoB | 761109 | p.Asp435Asn | missense_variant | 0.98 | rifampicin |
| rrs | 1472359 | n.514A>C | non_coding_transcript_exon_variant | 1.0 | streptomycin |
| katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
| pncA | 2289103 | p.Thr47Pro | missense_variant | 1.0 | pyrazinamide |
| embB | 4248003 | p.Gln497Pro | missense_variant | 0.99 | ethambutol |
| Gene | Chromosome position | Mutation | Type | Estimated fraction |
|---|---|---|---|---|
| gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
| gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
| gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
| mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
| rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
| Rv1258c | 1407069 | c.271delC | frameshift_variant | 1.0 |
| rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
| tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
| ndh | 2102497 | c.546T>C | synonymous_variant | 1.0 |
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
| Rv2752c | 3066099 | p.Met31Ile | missense_variant | 0.99 |
| ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
| Rv3083 | 3448348 | c.-156G>A | upstream_gene_variant | 0.99 |
| fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
| Rv3236c | 3613282 | c.-166G>A | upstream_gene_variant | 0.99 |
| embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
| embB | 4246508 | c.-6G>A | upstream_gene_variant | 1.0 |
| embB | 4248441 | p.Thr643Ile | missense_variant | 1.0 |
| aftB | 4268928 | c.-92C>T | upstream_gene_variant | 0.99 |
| aftB | 4269375 | c.-539G>A | upstream_gene_variant | 0.98 |
| ethA | 4326323 | c.1112_1150delGCATGATGCTTTCCGGCATCCCCAACATGGCCTACACGG | disruptive_inframe_deletion | 0.71 |
| whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
