| Variant ID: vg1225603321 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 25603321 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 124. )
CAGTAAGAACTCCTTCAGGTTTGCCAGTACTCACCCAGAAGCATTTCATAGCTGTCAGCCACAGAGTGACCCTGATCTGCCATCTCTTAAAATGCACACC[G/A]
GTGAATTTATCCGGCCTCAGTGCATCGGCAAAACCAGCCATAGTAAAATCACAGTGCCTATAATAAGGTTTTTGGATTGTTGAGATTATAGACATATAAT
ATTATATGTCTATAATCTCAACAATCCAAAAACCTTATTATAGGCACTGTGATTTTACTATGGCTGGTTTTGCCGATGCACTGAGGCCGGATAAATTCAC[C/T]
GGTGTGCATTTTAAGAGATGGCAGATCAGGGTCACTCTGTGGCTGACAGCTATGAAATGCTTCTGGGTGAGTACTGGCAAACCTGAAGGAGTTCTTACTG
| 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 | 57.60% | 7.60% | 4.61% | 30.13% | NA |
| All Indica | 2759 | 39.90% | 12.70% | 6.78% | 40.59% | NA |
| All Japonica | 1512 | 99.70% | 0.10% | 0.13% | 0.00% | NA |
| Aus | 269 | 1.90% | 0.40% | 4.09% | 93.68% | NA |
| Indica I | 595 | 85.50% | 1.80% | 1.85% | 10.76% | NA |
| Indica II | 465 | 13.10% | 12.30% | 7.31% | 67.31% | NA |
| Indica III | 913 | 27.10% | 23.10% | 9.97% | 39.87% | NA |
| Indica Intermediate | 786 | 36.30% | 9.00% | 6.49% | 48.22% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 98.30% | 0.80% | 0.83% | 0.00% | NA |
| VI/Aromatic | 96 | 56.20% | 3.10% | 14.58% | 26.04% | NA |
| Intermediate | 90 | 61.10% | 4.40% | 4.44% | 30.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1225603321 | G -> DEL | LOC_Os12g41280.1 | N | frameshift_variant | Average:17.845; most accessible tissue: Zhenshan97 panicle, score: 36.038 | N | N | N | N |
| vg1225603321 | G -> A | LOC_Os12g41280.1 | synonymous_variant ; p.Thr14Thr; LOW | synonymous_codon | Average:17.845; most accessible tissue: Zhenshan97 panicle, score: 36.038 | N | N | N | N |