Run ID: ERR502522
Sample name:
Date: 19-10-2023 20:26:31
Number of reads: 3743948
Percentage reads mapped: 91.82
Strain: lineage6.3.1
Drug-resistance: Other
| Drug | Resistance | Supporting mutations |
|---|---|---|
| Rifampicin | ||
| Isoniazid | ||
| Ethambutol | ||
| Pyrazinamide | ||
| Streptomycin | R | gid c.102delG (1.00) |
| Fluoroquinolones | ||
| Moxifloxacin | ||
| Ofloxacin | ||
| Levofloxacin | ||
| Ciprofloxacin | ||
| Aminoglycosides | ||
| Amikacin | ||
| Capreomycin | ||
| Kanamycin | ||
| Cycloserine | ||
| Ethionamide | ||
| Clofazimine | ||
| Para-aminosalicylic_acid | ||
| Delamanid | ||
| Bedaquiline | ||
| Linezolid |
| Lineage | Family | Main Spoligotype | RDs | Frequency |
|---|---|---|---|---|
| lineage6 | West-Africa 2 | AFRI_1 | RD702 | 1.0 |
| lineage6.3 | West-Africa 2 | AFRI_1 | RD702 | 1.0 |
| lineage6.3.1 | West-Africa 2 | AFRI_1 | RD702 | 1.0 |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
|---|---|---|---|---|---|
| gid | 4408100 | c.102delG | frameshift_variant | 1.0 | streptomycin |
| Gene | Chromosome position | Mutation | Type | Estimated fraction |
|---|---|---|---|---|
| gyrB | 6446 | p.Ala403Ser | missense_variant | 1.0 |
| gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
| gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
| gyrA | 9143 | c.1842T>C | synonymous_variant | 1.0 |
| gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
| fgd1 | 491668 | p.Lys296Glu | missense_variant | 1.0 |
| fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 |
| rpoB | 760969 | p.Ser388Leu | missense_variant | 1.0 |
| rpoB | 761723 | p.Glu639Asp | missense_variant | 1.0 |
| rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
| mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
| mmpL5 | 776100 | p.Thr794Ile | missense_variant | 0.99 |
| rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
| fbiC | 1302899 | c.-32A>G | upstream_gene_variant | 1.0 |
| atpE | 1461251 | c.207G>T | synonymous_variant | 1.0 |
| rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
| rrs | 1472172 | n.327T>C | non_coding_transcript_exon_variant | 0.11 |
| rrs | 1472781 | n.936C>T | non_coding_transcript_exon_variant | 0.12 |
| rrs | 1472793 | n.948A>T | non_coding_transcript_exon_variant | 0.12 |
| rrs | 1472956 | n.1111T>C | non_coding_transcript_exon_variant | 0.12 |
| rrs | 1472957 | n.1112C>T | non_coding_transcript_exon_variant | 0.12 |
| rrl | 1475881 | n.2224T>C | non_coding_transcript_exon_variant | 0.14 |
| rrl | 1475884 | n.2227A>G | non_coding_transcript_exon_variant | 0.17 |
| rrl | 1475897 | n.2240T>C | non_coding_transcript_exon_variant | 0.13 |
| rrl | 1475899 | n.2242G>A | non_coding_transcript_exon_variant | 0.13 |
| rrl | 1475943 | n.2286G>A | non_coding_transcript_exon_variant | 0.13 |
| rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.14 |
| rrl | 1476428 | n.2771C>T | non_coding_transcript_exon_variant | 0.17 |
| inhA | 1674243 | c.42A>C | synonymous_variant | 1.0 |
| inhA | 1674434 | p.Val78Ala | missense_variant | 1.0 |
| tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
| ndh | 2102694 | p.Val117Ile | missense_variant | 1.0 |
| katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 |
| katG | 2155503 | c.609C>T | synonymous_variant | 1.0 |
| PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
| Rv1979c | 2222308 | p.Asp286Gly | missense_variant | 1.0 |
| Rv1979c | 2222852 | p.Ala105Thr | missense_variant | 1.0 |
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
| kasA | 2518132 | c.18C>T | synonymous_variant | 1.0 |
| ald | 3086728 | c.-92C>T | upstream_gene_variant | 1.0 |
| ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
| ald | 3087084 | c.266delA | frameshift_variant | 1.0 |
| Rv3083 | 3449781 | c.1278G>A | synonymous_variant | 1.0 |
| fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
| fprA | 3475159 | p.Asn385Asp | missense_variant | 1.0 |
| rpoA | 3877696 | p.Thr271Ile | missense_variant | 1.0 |
| embC | 4240671 | p.Thr270Ile | missense_variant | 1.0 |
| embC | 4241843 | p.Leu661Ile | missense_variant | 0.98 |
| embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
| embA | 4244220 | c.988C>T | synonymous_variant | 1.0 |
| embA | 4244379 | p.Pro383Ser | missense_variant | 1.0 |
| embB | 4246864 | c.351C>T | synonymous_variant | 1.0 |
| embB | 4247646 | p.Glu378Ala | missense_variant | 1.0 |
| aftB | 4268477 | c.360C>T | synonymous_variant | 0.98 |
| aftB | 4269351 | c.-515C>T | upstream_gene_variant | 1.0 |
| ubiA | 4269387 | p.Glu149Asp | missense_variant | 1.0 |
| aftB | 4269522 | c.-686C>T | upstream_gene_variant | 1.0 |
| aftB | 4269606 | c.-770T>C | upstream_gene_variant | 1.0 |
| ethA | 4326465 | p.Ile337Val | missense_variant | 1.0 |
| whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
| gid | 4407588 | c.615A>G | synonymous_variant | 1.0 |
