| Variant ID: vg0208664960 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 8664960 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 327. )
GGGGAAACAAATTGCCCGAGACAACGTACGAGGCTAAGAAGATAGTCTGCCCGTTAGGACTGGAAGTTCATAAGATTCACGCATGTCCGAACGATTGTAT[C/T]
CTATATCGCGGTGAGGAGTATGAGAACCTAGAAGCATGCCCTGTTTGCAAAGCACTACGATACAAGATTAGACGGGACGATCCAGGAGAAGTTGACGGGC
GCCCGTCAACTTCTCCTGGATCGTCCCGTCTAATCTTGTATCGTAGTGCTTTGCAAACAGGGCATGCTTCTAGGTTCTCATACTCCTCACCGCGATATAG[G/A]
ATACAATCGTTCGGACATGCGTGAATCTTATGAACTTCCAGTCCTAACGGGCAGACTATCTTCTTAGCCTCGTACGTTGTCTCGGGCAATTTGTTTCCCC
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 24.80% | 0.30% | 1.95% | 72.87% | NA |
| All Indica | 2759 | 10.30% | 0.60% | 2.57% | 86.52% | NA |
| All Japonica | 1512 | 56.30% | 0.00% | 0.73% | 42.99% | NA |
| Aus | 269 | 5.20% | 0.00% | 2.97% | 91.82% | NA |
| Indica I | 595 | 12.10% | 0.20% | 3.36% | 84.37% | NA |
| Indica II | 465 | 4.90% | 1.10% | 1.94% | 92.04% | NA |
| Indica III | 913 | 8.10% | 0.80% | 2.08% | 89.05% | NA |
| Indica Intermediate | 786 | 14.80% | 0.40% | 2.93% | 81.93% | NA |
| Temperate Japonica | 767 | 80.20% | 0.00% | 0.65% | 19.17% | NA |
| Tropical Japonica | 504 | 30.60% | 0.00% | 0.40% | 69.05% | NA |
| Japonica Intermediate | 241 | 34.00% | 0.00% | 1.66% | 64.32% | NA |
| VI/Aromatic | 96 | 2.10% | 0.00% | 1.04% | 96.88% | NA |
| Intermediate | 90 | 24.40% | 0.00% | 1.11% | 74.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0208664960 | C -> T | LOC_Os02g15470.1 | synonymous_variant ; p.Ile139Ile; LOW | synonymous_codon | Average:4.469; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0208664960 | C -> DEL | LOC_Os02g15470.1 | N | frameshift_variant | Average:4.469; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |