Run ID: SRR13861146
Sample name:
Date: 2024-04-15T07:52:47.679471
Number of reads: 836069
Percentage reads mapped: 13.95
Median coverage: 29.0
Strain: lineage4.9
Spoligotype:
Drug-resistance: RR-TB
| Lineage | Family | RDs | Frequency |
|---|---|---|---|
| lineage4 | Euro-American | None | 1.0 |
| lineage4.9 | Euro-American (H37Rv-like) | None | 1.0 |
| Drug | Resistance | Supporting mutations | WHO confidence | Comment |
|---|---|---|---|---|
| rifampicin | rpoB | p.Pro439Arg | Assoc w R - Interim | Expert rule: Non-silent variants in RRDR of rpoB |
| isoniazid | ||||
| ethambutol | ||||
| pyrazinamide | ||||
| streptomycin | ||||
| fluoroquinolones | ||||
| moxifloxacin | ||||
| ofloxacin | ||||
| levofloxacin | ||||
| ciprofloxacin | ||||
| aminoglycosides | ||||
| amikacin | ||||
| capreomycin | ||||
| kanamycin | ||||
| cycloserine | ||||
| ethionamide | ||||
| clofazimine | ||||
| para-aminosalicylic_acid | ||||
| delamanid | ||||
| bedaquiline | ||||
| linezolid |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
|---|---|---|---|---|---|---|---|
| rpoB | 761122 | p.Pro439Arg | missense_variant | 0.84 | rifampicin | Assoc w R - Interim | Expert rule: Non-silent variants in RRDR of rpoB |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
|---|---|---|---|---|---|---|
| gyrB | 5192 | c.-48C>G | upstream_gene_variant | 1.0 | levofloxacin | |
| moxifloxacin | ||||||
| gyrA | 8111 | c.810G>C | synonymous_variant | 0.24 | levofloxacin | |
| moxifloxacin | ||||||
| gyrA | 8225 | c.924T>C | synonymous_variant | 0.18 | levofloxacin | |
| moxifloxacin | ||||||
| gyrA | 8597 | c.1296C>G | synonymous_variant | 0.17 | levofloxacin | |
| moxifloxacin | ||||||
| gyrA | 8603 | c.1302A>G | synonymous_variant | 0.18 | levofloxacin | Not assoc w R - Interim |
| moxifloxacin | Not assoc w R - Interim | |||||
| gyrA | 8619 | c.1318T>C | synonymous_variant | 0.2 | levofloxacin | Not assoc w R - Interim |
| moxifloxacin | Not assoc w R - Interim | |||||
| gyrA | 8624 | c.1323G>C | synonymous_variant | 0.21 | levofloxacin | |
| moxifloxacin | ||||||
| gyrA | 9658 | c.2357_2358insT | frameshift_variant | 0.97 | levofloxacin | |
| moxifloxacin | ||||||
| fgd1 | 490779 | c.-4A>T | upstream_gene_variant | 1.0 | clofazimine | |
| pretomanid | ||||||
| delamanid | ||||||
| Rv0565c | 657379 | p.Arg31His | missense_variant | 0.97 | ethionamide | |
| rpoB | 760041 | p.Gly79Arg | missense_variant | 1.0 | rifampicin | |
| rpoB | 760652 | c.846C>A | synonymous_variant | 0.91 | rifampicin | |
| rpoB | 760721 | c.915C>G | synonymous_variant | 0.2 | rifampicin | |
| rpoB | 760946 | c.1140A>G | synonymous_variant | 0.21 | rifampicin | Not assoc w R - Interim |
| rpoB | 761015 | c.1209G>C | synonymous_variant | 0.19 | rifampicin | Not assoc w R - Interim |
| rpoB | 761021 | c.1215G>C | synonymous_variant | 0.21 | rifampicin | |
| rpoB | 761027 | c.1221A>G | synonymous_variant | 0.2 | rifampicin | Not assoc w R - Interim |
| rpoB | 761036 | c.1230G>C | synonymous_variant | 0.19 | rifampicin | Not assoc w R - Interim |
| rpoB | 761037 | c.1231T>C | synonymous_variant | 0.19 | rifampicin | Not assoc w R - Interim |
| rpoB | 761051 | c.1245G>T | synonymous_variant | 0.17 | rifampicin | Not assoc w R - Interim |
| rpoB | 761054 | c.1248G>C | synonymous_variant | 0.17 | rifampicin | Not assoc w R - Interim |
| rpoB | 761057 | c.1251G>C | synonymous_variant | 0.17 | rifampicin | Not assoc w R - Interim |
| rpoB | 761060 | c.1254C>G | synonymous_variant | 0.17 | rifampicin | Not assoc w R - Interim |
| rpoB | 761063 | c.1257C>G | synonymous_variant | 0.18 | rifampicin | Not assoc w R - Interim |
| rpoB | 761094 | c.1288C>T | synonymous_variant | 0.18 | rifampicin | Not assoc w R - Interim |
| rpoB | 761097 | c.1291_1292delAGinsTC | synonymous_variant | 0.17 | rifampicin | |
| rpoB | 761102 | c.1296A>G | synonymous_variant | 0.18 | rifampicin | |
| rpoC | 765421 | c.2052C>G | synonymous_variant | 0.25 | rifampicin | Not assoc w R - Interim |
| rpoC | 765451 | c.2082C>G | synonymous_variant | 0.27 | rifampicin | |
| rpoC | 765452 | c.2083_2085delGCCinsTG | frameshift_variant&missense_variant | 0.27 | rifampicin | |
| rpoC | 765478 | c.2109T>C | synonymous_variant | 0.29 | rifampicin | Not assoc w R - Interim |
| rpoC | 765499 | c.2130C>G | synonymous_variant | 0.26 | rifampicin | Not assoc w R - Interim |
| rpoC | 765508 | c.2139C>G | synonymous_variant | 0.25 | rifampicin | Not assoc w R - Interim |
| rpoC | 765541 | c.2172C>G | synonymous_variant | 0.24 | rifampicin | |
| rpoC | 765553 | c.2184C>T | synonymous_variant | 0.23 | rifampicin | Not assoc w R - Interim |
| rpoC | 765556 | c.2187G>C | synonymous_variant | 0.21 | rifampicin | |
| rpoC | 765559 | c.2190G>C | synonymous_variant | 0.22 | rifampicin | |
| mmpL5 | 775929 | p.Asn851Ile | missense_variant | 0.88 | clofazimine | |
| bedaquiline | ||||||
| mmpS5 | 778941 | c.-36A>G | upstream_gene_variant | 1.0 | clofazimine | Uncertain significance |
| bedaquiline | Uncertain significance | |||||
| rpsL | 781149 | c.-411C>T | upstream_gene_variant | 0.96 | streptomycin | |
| rpsL | 781277 | c.-283G>T | upstream_gene_variant | 1.0 | streptomycin | |
| fbiC | 1303674 | c.744C>G | synonymous_variant | 0.27 | clofazimine | |
| pretomanid | ||||||
| delamanid | ||||||
| fbiC | 1303686 | c.756C>G | synonymous_variant | 0.24 | clofazimine | |
| pretomanid | ||||||
| delamanid | ||||||
| embR | 1417376 | c.-29T>C | upstream_gene_variant | 1.0 | ethambutol | |
| rrl | 1473740 | n.83G>A | non_coding_transcript_exon_variant | 0.9 | capreomycin | |
| linezolid | ||||||
| rrl | 1473813 | n.156C>T | non_coding_transcript_exon_variant | 0.15 | capreomycin | |
| linezolid | ||||||
| rrl | 1474574 | n.917A>T | non_coding_transcript_exon_variant | 0.9 | capreomycin | |
| linezolid | ||||||
| rrl | 1475061 | n.1404C>T | non_coding_transcript_exon_variant | 0.19 | capreomycin | Uncertain significance |
| linezolid | ||||||
| rrl | 1475249 | n.1592T>C | non_coding_transcript_exon_variant | 0.21 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1475252 | n.1595C>T | non_coding_transcript_exon_variant | 0.23 | capreomycin | |
| linezolid | ||||||
| rrl | 1475638 | n.1981C>T | non_coding_transcript_exon_variant | 0.2 | capreomycin | |
| linezolid | ||||||
| rrl | 1475642 | n.1985T>C | non_coding_transcript_exon_variant | 0.19 | capreomycin | |
| linezolid | ||||||
| rrl | 1475657 | n.2000A>G | non_coding_transcript_exon_variant | 0.2 | capreomycin | |
| linezolid | ||||||
| rrl | 1475659 | n.2002G>T | non_coding_transcript_exon_variant | 0.18 | capreomycin | |
| linezolid | ||||||
| rrl | 1476281 | n.2624T>C | non_coding_transcript_exon_variant | 0.2 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rpsA | 1833661 | c.120A>G | synonymous_variant | 0.21 | pyrazinamide | |
| rpsA | 1833667 | c.126C>G | synonymous_variant | 0.2 | pyrazinamide | |
| rpsA | 1833724 | c.183C>G | synonymous_variant | 0.2 | pyrazinamide | |
| rpsA | 1833727 | c.186G>C | synonymous_variant | 0.2 | pyrazinamide | |
| rpsA | 1833742 | c.201A>G | synonymous_variant | 0.21 | pyrazinamide | |
| rpsA | 1833745 | c.204G>C | synonymous_variant | 0.21 | pyrazinamide | |
| rpsA | 1833787 | c.246C>G | synonymous_variant | 0.21 | pyrazinamide | |
| rpsA | 1833799 | c.258C>G | synonymous_variant | 0.22 | pyrazinamide | |
| rpsA | 1833838 | c.297G>C | synonymous_variant | 0.18 | pyrazinamide | |
| rpsA | 1833841 | c.300C>G | synonymous_variant | 0.18 | pyrazinamide | |
| rpsA | 1833928 | c.387G>C | synonymous_variant | 0.21 | pyrazinamide | |
| rpsA | 1833940 | c.399C>G | synonymous_variant | 0.23 | pyrazinamide | |
| rpsA | 1834610 | p.Arg357Gly | missense_variant | 0.87 | pyrazinamide | |
| tsnR | 1854354 | p.Leu250Gln | missense_variant | 1.0 | linezolid | |
| ndh | 2101828 | c.1215C>T | synonymous_variant | 1.0 | ethionamide | |
| delamanid | ||||||
| isoniazid | ||||||
| PPE35 | 2168706 | p.Ser636Phe | missense_variant | 1.0 | pyrazinamide | |
| pncA | 2289887 | c.-646A>C | upstream_gene_variant | 0.95 | pyrazinamide | |
| folC | 2746838 | p.Ala254Glu | missense_variant | 1.0 | para-aminosalicylic_acid | |
| Rv2477c | 2783062 | c.981C>G | synonymous_variant | 0.19 | ethambutol | |
| moxifloxacin | ||||||
| streptomycin | ||||||
| levofloxacin | ||||||
| kanamycin | ||||||
| rifampicin | ||||||
| amikacin | ||||||
| Rv2477c | 2783110 | c.933C>A | synonymous_variant | 0.22 | ethambutol | |
| moxifloxacin | ||||||
| streptomycin | ||||||
| levofloxacin | ||||||
| kanamycin | ||||||
| rifampicin | ||||||
| amikacin | ||||||
| Rv2477c | 2783116 | c.927T>C | synonymous_variant | 0.22 | ethambutol | |
| moxifloxacin | ||||||
| streptomycin | ||||||
| levofloxacin | ||||||
| kanamycin | ||||||
| rifampicin | ||||||
| amikacin | ||||||
| Rv2477c | 2783140 | c.903C>G | synonymous_variant | 0.19 | ethambutol | |
| moxifloxacin | ||||||
| streptomycin | ||||||
| levofloxacin | ||||||
| kanamycin | ||||||
| rifampicin | ||||||
| amikacin | ||||||
| Rv2477c | 2783158 | c.885A>G | synonymous_variant | 0.21 | ethambutol | |
| moxifloxacin | ||||||
| streptomycin | ||||||
| levofloxacin | ||||||
| kanamycin | ||||||
| rifampicin | ||||||
| amikacin | ||||||
| Rv2477c | 2783185 | c.858G>C | synonymous_variant | 0.21 | ethambutol | |
| moxifloxacin | ||||||
| streptomycin | ||||||
| levofloxacin | ||||||
| kanamycin | ||||||
| rifampicin | ||||||
| amikacin | ||||||
| Rv2477c | 2783316 | p.Thr243Ala | missense_variant | 0.94 | ethambutol | |
| moxifloxacin | ||||||
| streptomycin | ||||||
| levofloxacin | ||||||
| kanamycin | ||||||
| rifampicin | ||||||
| amikacin | ||||||
| Rv2477c | 2783641 | c.402G>C | synonymous_variant | 0.16 | ethambutol | |
| moxifloxacin | ||||||
| streptomycin | ||||||
| levofloxacin | ||||||
| kanamycin | ||||||
| rifampicin | ||||||
| amikacin | ||||||
| Rv2477c | 2783659 | c.384A>G | synonymous_variant | 0.18 | ethambutol | |
| moxifloxacin | ||||||
| streptomycin | ||||||
| levofloxacin | ||||||
| kanamycin | ||||||
| rifampicin | ||||||
| amikacin | ||||||
| ribD | 2987500 | p.Gly221Asp | missense_variant | 1.0 | para-aminosalicylic_acid | |
| thyX | 3068082 | c.-137T>C | upstream_gene_variant | 1.0 | para-aminosalicylic_acid | |
| fbiD | 3338954 | c.-164A>G | upstream_gene_variant | 1.0 | clofazimine | |
| pretomanid | ||||||
| delamanid | ||||||
| fbiD | 3339235 | p.Leu40Val | missense_variant | 1.0 | clofazimine | |
| pretomanid | ||||||
| delamanid | ||||||
| fbiD | 3339406 | p.Thr97Ala | missense_variant | 1.0 | clofazimine | |
| pretomanid | ||||||
| delamanid | ||||||
| Rv3083 | 3448625 | p.Leu41Gln | missense_variant | 1.0 | ethionamide | |
| lpqB | 3624203 | c.708C>T | synonymous_variant | 0.89 | bedaquiline | |
| rifampicin | ||||||
| mtrB | 3626461 | c.153A>G | synonymous_variant | 1.0 | bedaquiline | |
| rifampicin | Not assoc w R - Interim | |||||
| mtrB | 3626554 | c.60A>T | synonymous_variant | 1.0 | bedaquiline | |
| rifampicin | ||||||
| mtrA | 3627267 | p.Glu28Val | missense_variant | 0.88 | bedaquiline | |
| rifampicin | ||||||
| fbiB | 3642247 | p.Asn238Thr | missense_variant | 1.0 | clofazimine | |
| pretomanid | ||||||
| delamanid | ||||||
| fbiB | 3642283 | p.Glu250Ala | missense_variant | 1.0 | clofazimine | |
| pretomanid | ||||||
| delamanid | ||||||
| rpoA | 3877818 | c.690A>G | synonymous_variant | 0.25 | rifampicin | Not assoc w R - Interim |
| rpoA | 3877839 | c.669G>C | synonymous_variant | 0.21 | rifampicin | Not assoc w R - Interim |
| rpoA | 3878337 | c.171T>C | synonymous_variant | 0.23 | rifampicin | Not assoc w R - Interim |
| rpoA | 3878346 | c.162T>C | synonymous_variant | 0.21 | rifampicin | |
| rpoA | 3878968 | c.-461T>G | upstream_gene_variant | 0.19 | rifampicin | |
| rpoA | 3878989 | c.-482G>C | upstream_gene_variant | 0.21 | rifampicin | |
| rpoA | 3879037 | c.-530G>C | upstream_gene_variant | 0.21 | rifampicin | |
| rpoA | 3879040 | c.-533G>C | upstream_gene_variant | 0.21 | rifampicin | |
| rpoA | 3879049 | c.-542A>G | upstream_gene_variant | 0.25 | rifampicin | |
| clpC1 | 4039268 | c.1437C>G | synonymous_variant | 0.15 | pyrazinamide | |
| clpC1 | 4039388 | c.1317C>A | synonymous_variant | 0.17 | pyrazinamide | |
| clpC1 | 4039391 | c.1314T>G | synonymous_variant | 0.17 | pyrazinamide | |
| clpC1 | 4039483 | c.1221_1222insC | frameshift_variant | 1.0 | pyrazinamide | |
| clpC1 | 4039616 | c.1089G>C | synonymous_variant | 0.16 | pyrazinamide | |
| clpC1 | 4039622 | c.1083C>G | synonymous_variant | 0.17 | pyrazinamide | |
| glpK | 4139747 | p.Asp3Glu | missense_variant | 1.0 | ethambutol | |
| moxifloxacin | ||||||
| streptomycin | ||||||
| levofloxacin | ||||||
| rifampicin | ||||||
| isoniazid | ||||||
| embA | 4243843 | c.613dupG | frameshift_variant | 1.0 | ethambutol | Uncertain significance |
| embA | 4244833 | p.Val534Ala | missense_variant | 1.0 | ethambutol | |
| embA | 4245735 | p.Ala835Ser | missense_variant | 0.97 | ethambutol | |
| aftB | 4267994 | p.Met281Ile | missense_variant | 1.0 | ethambutol |
