| Variant ID: vg1225603322 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 25603322 |
| 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: 281. )
AGTAAGAACTCCTTCAGGTTTGCCAGTACTCACCCAGAAGCATTTCATAGCTGTCAGCCACAGAGTGACCCTGATCTGCCATCTCTTAAAATGCACACCG[G/A]
TGAATTTATCCGGCCTCAGTGCATCGGCAAAACCAGCCATAGTAAAATCACAGTGCCTATAATAAGGTTTTTGGATTGTTGAGATTATAGACATATAATG
CATTATATGTCTATAATCTCAACAATCCAAAAACCTTATTATAGGCACTGTGATTTTACTATGGCTGGTTTTGCCGATGCACTGAGGCCGGATAAATTCA[C/T]
CGGTGTGCATTTTAAGAGATGGCAGATCAGGGTCACTCTGTGGCTGACAGCTATGAAATGCTTCTGGGTGAGTACTGGCAAACCTGAAGGAGTTCTTACT
| 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 | 70.80% | 0.10% | 1.63% | 27.42% | NA |
| All Indica | 2759 | 61.10% | 0.00% | 2.21% | 36.72% | NA |
| All Japonica | 1512 | 99.80% | 0.10% | 0.13% | 0.00% | NA |
| Aus | 269 | 8.60% | 0.00% | 2.23% | 89.22% | NA |
| Indica I | 595 | 90.40% | 0.00% | 0.17% | 9.41% | NA |
| Indica II | 465 | 35.90% | 0.00% | 1.29% | 62.80% | NA |
| Indica III | 913 | 60.80% | 0.00% | 3.94% | 35.27% | NA |
| Indica Intermediate | 786 | 54.10% | 0.00% | 2.29% | 43.64% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.80% | 0.00% | 0.20% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.20% | 0.40% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 63.50% | 5.20% | 6.25% | 25.00% | NA |
| Intermediate | 90 | 75.60% | 1.10% | 2.22% | 21.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1225603322 | G -> DEL | LOC_Os12g41280.1 | N | frameshift_variant | Average:17.845; most accessible tissue: Zhenshan97 panicle, score: 36.038 | N | N | N | N |
| vg1225603322 | G -> A | LOC_Os12g41280.1 | missense_variant ; p.Thr14Ile; MODERATE | nonsynonymous_codon ; T14I | Average:17.845; most accessible tissue: Zhenshan97 panicle, score: 36.038 | unknown | unknown | DELETERIOUS | 0.02 |