| Variant ID: vg1212666273 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 12666273 |
| 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: 268. )
TGGTTGACAAAGCAATTCGCCTTGAAGACAAGAAGAACAGGATGGATAACCGTAAAAGGAAAATGACTGTTTTCCAGGAGGCACAAGGTAGTAGCCAGAG[G/A]
CAGCGTATCAAGCCACTCCAAATTGGTGAATCTTCTTCCGCTGGTCAAGGACAGTCGCAACTGTTGAACATCGGTGGTGAGATCAAATTAGAGACTAATG
CATTAGTCTCTAATTTGATCTCACCACCGATGTTCAACAGTTGCGACTGTCCTTGACCAGCGGAAGAAGATTCACCAATTTGGAGTGGCTTGATACGCTG[C/T]
CTCTGGCTACTACCTTGTGCCTCCTGGAAAACAGTCATTTTCCTTTTACGGTTATCCATCCTGTTCTTCTTGTCTTCAAGGCGAATTGCTTTGTCAACCA
| 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 | 78.30% | 0.90% | 2.09% | 18.71% | NA |
| All Indica | 2759 | 81.50% | 1.30% | 1.88% | 15.33% | NA |
| All Japonica | 1512 | 69.80% | 0.00% | 2.31% | 27.84% | NA |
| Aus | 269 | 91.40% | 1.90% | 1.49% | 5.20% | NA |
| Indica I | 595 | 70.40% | 0.00% | 2.18% | 27.39% | NA |
| Indica II | 465 | 83.20% | 0.00% | 1.51% | 15.27% | NA |
| Indica III | 913 | 87.60% | 2.80% | 1.64% | 7.89% | NA |
| Indica Intermediate | 786 | 81.70% | 1.30% | 2.16% | 14.89% | NA |
| Temperate Japonica | 767 | 83.60% | 0.00% | 0.39% | 16.04% | NA |
| Tropical Japonica | 504 | 57.70% | 0.00% | 4.56% | 37.70% | NA |
| Japonica Intermediate | 241 | 51.50% | 0.00% | 3.73% | 44.81% | NA |
| VI/Aromatic | 96 | 87.50% | 0.00% | 2.08% | 10.42% | NA |
| Intermediate | 90 | 75.60% | 0.00% | 6.67% | 17.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1212666273 | G -> DEL | LOC_Os12g22430.1 | N | frameshift_variant | Average:4.447; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg1212666273 | G -> A | LOC_Os12g22430.1 | synonymous_variant ; p.Arg246Arg; LOW | synonymous_codon | Average:4.447; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |