| Variant ID: vg1222420013 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 22420013 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.89, A: 0.13, others allele: 0.00, population size: 63. )
ACAGATTAATTAGGCTTAATAGATTCGTCTCGCAGTTTATATGCGGAATTTATAATTTGTTTTGTTATTAGTCTACATTTAATACTTTAAATATGTTTCT[G/A]
TATACTTAAAAAAGATTTGGCACACGAACTAAACACAGCCTAAATAAAGTGCTCAAGAATATACATGAGATTATATTCACAACATTGCCCATTCAGGTAG
CTACCTGAATGGGCAATGTTGTGAATATAATCTCATGTATATTCTTGAGCACTTTATTTAGGCTGTGTTTAGTTCGTGTGCCAAATCTTTTTTAAGTATA[C/T]
AGAAACATATTTAAAGTATTAAATGTAGACTAATAACAAAACAAATTATAAATTCCGCATATAAACTGCGAGACGAATCTATTAAGCCTAATTAATCTGT
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 38.20% | 17.90% | 0.30% | 43.59% | NA |
| All Indica | 2759 | 9.40% | 29.50% | 0.47% | 60.67% | NA |
| All Japonica | 1512 | 86.20% | 0.70% | 0.00% | 13.10% | NA |
| Aus | 269 | 33.50% | 4.50% | 0.37% | 61.71% | NA |
| Indica I | 595 | 10.60% | 29.90% | 0.17% | 59.33% | NA |
| Indica II | 465 | 4.30% | 17.40% | 0.86% | 77.42% | NA |
| Indica III | 913 | 9.70% | 35.30% | 0.33% | 54.65% | NA |
| Indica Intermediate | 786 | 11.10% | 29.50% | 0.64% | 58.78% | NA |
| Temperate Japonica | 767 | 91.40% | 0.10% | 0.00% | 8.47% | NA |
| Tropical Japonica | 504 | 77.20% | 1.20% | 0.00% | 21.63% | NA |
| Japonica Intermediate | 241 | 88.80% | 1.20% | 0.00% | 9.96% | NA |
| VI/Aromatic | 96 | 93.80% | 2.10% | 0.00% | 4.17% | NA |
| Intermediate | 90 | 67.80% | 12.20% | 0.00% | 20.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1222420013 | G -> DEL | N | N | silent_mutation | Average:11.11; most accessible tissue: Callus, score: 63.722 | N | N | N | N |
| vg1222420013 | G -> A | LOC_Os12g36600.1 | downstream_gene_variant ; 4397.0bp to feature; MODIFIER | silent_mutation | Average:11.11; most accessible tissue: Callus, score: 63.722 | N | N | N | N |
| vg1222420013 | G -> A | LOC_Os12g36610.1 | downstream_gene_variant ; 748.0bp to feature; MODIFIER | silent_mutation | Average:11.11; most accessible tissue: Callus, score: 63.722 | N | N | N | N |
| vg1222420013 | G -> A | LOC_Os12g36620.1 | intron_variant ; MODIFIER | silent_mutation | Average:11.11; most accessible tissue: Callus, score: 63.722 | N | N | N | N |