| Variant ID: vg0136521260 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 36521260 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CAAAGCCTCCCATAGAAAAATTCAGTATATCTATGAAAAATTCAGTAAATACTGGTGCGTATCAAAGTTCAGTCTATGAATCACTGTGGAAAGATTCAGT[A/T]
TAGATGTGGAAAATGCAGTATATGCTATCGTCCAATAAAGTAGAGAATAAAGCTCCCCACATAAAAATTCAGTATATACTATTGCCTAACAGAGAGTTCA
TGAACTCTCTGTTAGGCAATAGTATATACTGAATTTTTATGTGGGGAGCTTTATTCTCTACTTTATTGGACGATAGCATATACTGCATTTTCCACATCTA[T/A]
ACTGAATCTTTCCACAGTGATTCATAGACTGAACTTTGATACGCACCAGTATTTACTGAATTTTTCATAGATATACTGAATTTTTCTATGGGAGGCTTTG
| Populations | Population Size | Frequency of A(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 34.30% | 2.00% | 4.78% | 58.93% | NA |
| All Indica | 2759 | 3.50% | 0.00% | 3.73% | 92.75% | NA |
| All Japonica | 1512 | 97.00% | 0.30% | 0.13% | 2.65% | NA |
| Aus | 269 | 0.70% | 0.40% | 42.01% | 56.88% | NA |
| Indica I | 595 | 1.30% | 0.00% | 2.35% | 96.30% | NA |
| Indica II | 465 | 4.10% | 0.00% | 3.01% | 92.90% | NA |
| Indica III | 913 | 2.20% | 0.00% | 3.72% | 94.09% | NA |
| Indica Intermediate | 786 | 6.20% | 0.10% | 5.22% | 88.42% | NA |
| Temperate Japonica | 767 | 98.70% | 0.10% | 0.00% | 1.17% | NA |
| Tropical Japonica | 504 | 96.80% | 0.00% | 0.20% | 2.98% | NA |
| Japonica Intermediate | 241 | 91.70% | 1.20% | 0.41% | 6.64% | NA |
| VI/Aromatic | 96 | 6.20% | 82.30% | 5.21% | 6.25% | NA |
| Intermediate | 90 | 56.70% | 10.00% | 3.33% | 30.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0136521260 | A -> T | LOC_Os01g63030.1 | downstream_gene_variant ; 4647.0bp to feature; MODIFIER | silent_mutation | Average:5.515; most accessible tissue: Callus, score: 15.99 | N | N | N | N |
| vg0136521260 | A -> T | LOC_Os01g63040.1 | intron_variant ; MODIFIER | silent_mutation | Average:5.515; most accessible tissue: Callus, score: 15.99 | N | N | N | N |
| vg0136521260 | A -> DEL | N | N | silent_mutation | Average:5.515; most accessible tissue: Callus, score: 15.99 | N | N | N | N |