Run ID: SRR5817476
Sample name:
Date: 04-04-2023 11:12:56
Number of reads: 17550740
Percentage reads mapped: 96.64
Strain: lineage1.1.2
Drug-resistance: Pre-XDR-TB
| Drug | Resistance | Supporting mutations |
|---|
| Lineage | Family | Main Spoligotype | RDs | Frequency |
|---|---|---|---|---|
| lineage1 | Indo-Oceanic | EAI | RD239 | 1.0 |
| lineage1.1 | Indo-Oceanic | EAI3;EAI4;EAI5;EAI6 | RD239 | 1.0 |
| lineage1.1.2 | Indo-Oceanic | EAI3;EAI5 | RD239 | 1.0 |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
|---|---|---|---|---|---|
| gyrA | 7582 | p.Asp94Ala | missense_variant | 1.0 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
| rpoB | 761155 | p.Ser450Trp | missense_variant | 1.0 | rifampicin |
| rpsL | 781687 | p.Lys43Arg | missense_variant | 1.0 | streptomycin |
| rrs | 1473246 | n.1401A>G | non_coding_transcript_exon_variant | 1.0 | kanamycin, capreomycin, aminoglycosides, amikacin |
| inhA | 1674048 | c.-154G>A | upstream_gene_variant | 0.99 | isoniazid, ethionamide |
| katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
| embB | 4247496 | p.Asp328Gly | missense_variant | 1.0 | ethambutol |
| embB | 4247729 | p.Gly406Ser | missense_variant | 1.0 | ethambutol |
| pncA | 2284911 | c.473_*3769del | frameshift_variant&stop_lost&splice_region_variant | 1.0 | pyrazinamide |
| Gene | Chromosome position | Mutation | Type | Estimated fraction |
|---|---|---|---|---|
| gyrB | 6112 | p.Met291Ile | missense_variant | 1.0 |
| gyrB | 6124 | c.885C>T | synonymous_variant | 1.0 |
| gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
| gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
| gyrA | 8452 | p.Ala384Val | missense_variant | 1.0 |
| gyrA | 9143 | c.1842T>C | synonymous_variant | 0.99 |
| gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
| fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 |
| rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
| rpoC | 763884 | p.Ala172Val | missense_variant | 0.99 |
| rpoC | 763886 | c.517C>A | synonymous_variant | 0.99 |
| rpoC | 764925 | p.Gly519Asp | missense_variant | 0.99 |
| rpoC | 765171 | p.Pro601Leu | missense_variant | 1.0 |
| rpoC | 765988 | c.2619G>A | synonymous_variant | 1.0 |
| mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
| mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 |
| mmpR5 | 779127 | c.139dupG | frameshift_variant | 1.0 |
| rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
| embR | 1417019 | p.Cys110Tyr | missense_variant | 1.0 |
| embR | 1417029 | p.Asp107Asn | missense_variant | 0.99 |
| rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
| tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
| katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 |
| PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
| PPE35 | 2167983 | p.Gly877Asp | missense_variant | 0.99 |
| Rv1979c | 2222308 | p.Asp286Gly | missense_variant | 0.99 |
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
| pncA | 2288768 | p.Asp158Glu | missense_variant | 0.8 |
| kasA | 2518132 | c.18C>T | synonymous_variant | 0.99 |
| ahpC | 2726051 | c.-142G>A | upstream_gene_variant | 1.0 |
| ahpC | 2726468 | c.276G>A | synonymous_variant | 1.0 |
| Rv2752c | 3064632 | c.1560C>T | synonymous_variant | 1.0 |
| thyX | 3067491 | p.Ala152Val | missense_variant | 1.0 |
| thyX | 3067949 | c.-4C>T | upstream_gene_variant | 0.99 |
| thyA | 3074040 | c.432G>A | synonymous_variant | 1.0 |
| ald | 3086788 | c.-32T>C | upstream_gene_variant | 0.99 |
| ald | 3087219 | p.Ser134Gly | missense_variant | 1.0 |
| Rv3083 | 3448714 | p.Asp71His | missense_variant | 1.0 |
| fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 0.99 |
| fprA | 3474597 | c.591C>A | synonymous_variant | 1.0 |
| fprA | 3475159 | p.Asn385Asp | missense_variant | 1.0 |
| fbiA | 3640446 | c.-97A>T | upstream_gene_variant | 0.99 |
| clpC1 | 4040517 | p.Val63Ala | missense_variant | 1.0 |
| embC | 4240671 | p.Thr270Ile | missense_variant | 1.0 |
| embC | 4241042 | p.Asn394Asp | missense_variant | 1.0 |
| embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
| embA | 4243848 | p.Val206Met | missense_variant | 1.0 |
| embA | 4245969 | p.Pro913Ser | missense_variant | 0.99 |
| embB | 4247646 | p.Glu378Ala | missense_variant | 1.0 |
| ubiA | 4269387 | p.Glu149Asp | missense_variant | 1.0 |
| aftB | 4269606 | c.-770T>C | upstream_gene_variant | 0.99 |
| ethA | 4326265 | p.Cys403Trp | missense_variant | 0.99 |
| whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
| whiB6 | 4338603 | c.-82C>T | upstream_gene_variant | 1.0 |
| gid | 4407588 | c.615A>G | synonymous_variant | 1.0 |
| gid | 4407873 | c.330G>T | synonymous_variant | 1.0 |
| thyA | 3073407 | c.431_*272del | frameshift_variant&stop_lost&splice_region_variant | 1.0 |
