| Variant ID: vg1212666313 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 12666313 |
| 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: 277. )
GATGGATAACCGTAAAAGGAAAATGACTGTTTTCCAGGAGGCACAAGGTAGTAGCCAGAGGCAGCGTATCAAGCCACTCCAAATTGGTGAATCTTCTTCC[G/A]
CTGGTCAAGGACAGTCGCAACTGTTGAACATCGGTGGTGAGATCAAATTAGAGACTAATGAAAGTAATGAAGTAAACATCGAGCAAGCTAATCAGCCGGT
ACCGGCTGATTAGCTTGCTCGATGTTTACTTCATTACTTTCATTAGTCTCTAATTTGATCTCACCACCGATGTTCAACAGTTGCGACTGTCCTTGACCAG[C/T]
GGAAGAAGATTCACCAATTTGGAGTGGCTTGATACGCTGCCTCTGGCTACTACCTTGTGCCTCCTGGAAAACAGTCATTTTCCTTTTACGGTTATCCATC
| 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 | 81.70% | 0.10% | 0.99% | 17.22% | NA |
| All Indica | 2759 | 83.50% | 0.10% | 1.09% | 15.33% | NA |
| All Japonica | 1512 | 75.90% | 0.00% | 0.79% | 23.35% | NA |
| Aus | 269 | 95.90% | 0.00% | 0.37% | 3.72% | NA |
| Indica I | 595 | 70.90% | 0.00% | 1.85% | 27.23% | NA |
| Indica II | 465 | 83.70% | 0.00% | 0.65% | 15.70% | NA |
| Indica III | 913 | 91.50% | 0.20% | 0.55% | 7.78% | NA |
| Indica Intermediate | 786 | 83.60% | 0.10% | 1.40% | 14.89% | NA |
| Temperate Japonica | 767 | 84.70% | 0.00% | 0.13% | 15.12% | NA |
| Tropical Japonica | 504 | 69.20% | 0.00% | 1.98% | 28.77% | NA |
| Japonica Intermediate | 241 | 61.40% | 0.00% | 0.41% | 38.17% | NA |
| VI/Aromatic | 96 | 87.50% | 0.00% | 2.08% | 10.42% | NA |
| Intermediate | 90 | 76.70% | 1.10% | 2.22% | 20.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1212666313 | G -> DEL | LOC_Os12g22430.1 | N | frameshift_variant | Average:5.272; most accessible tissue: Zhenshan97 panicle, score: 16.188 | N | N | N | N |
| vg1212666313 | G -> A | LOC_Os12g22430.1 | missense_variant ; p.Ala260Thr; MODERATE | nonsynonymous_codon ; A260T | Average:5.272; most accessible tissue: Zhenshan97 panicle, score: 16.188 | unknown | unknown | TOLERATED | 0.11 |