| Variant ID: vg0208664969 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 8664969 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 331. )
AATTGCCCGAGACAACGTACGAGGCTAAGAAGATAGTCTGCCCGTTAGGACTGGAAGTTCATAAGATTCACGCATGTCCGAACGATTGTATCCTATATCG[C/T]
GGTGAGGAGTATGAGAACCTAGAAGCATGCCCTGTTTGCAAAGCACTACGATACAAGATTAGACGGGACGATCCAGGAGAAGTTGACGGGCAGCTAACAA
TTGTTAGCTGCCCGTCAACTTCTCCTGGATCGTCCCGTCTAATCTTGTATCGTAGTGCTTTGCAAACAGGGCATGCTTCTAGGTTCTCATACTCCTCACC[G/A]
CGATATAGGATACAATCGTTCGGACATGCGTGAATCTTATGAACTTCCAGTCCTAACGGGCAGACTATCTTCTTAGCCTCGTACGTTGTCTCGGGCAATT
| 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 | 24.50% | 0.10% | 7.07% | 68.32% | NA |
| All Indica | 2759 | 12.30% | 0.10% | 10.22% | 77.38% | NA |
| All Japonica | 1512 | 51.70% | 0.10% | 2.18% | 46.03% | NA |
| Aus | 269 | 3.70% | 0.40% | 3.35% | 92.57% | NA |
| Indica I | 595 | 12.30% | 0.30% | 9.75% | 77.65% | NA |
| Indica II | 465 | 8.60% | 0.00% | 10.32% | 81.08% | NA |
| Indica III | 913 | 13.30% | 0.10% | 10.30% | 76.34% | NA |
| Indica Intermediate | 786 | 13.40% | 0.00% | 10.43% | 76.21% | NA |
| Temperate Japonica | 767 | 77.30% | 0.00% | 1.96% | 20.73% | NA |
| Tropical Japonica | 504 | 21.80% | 0.20% | 2.58% | 75.40% | NA |
| Japonica Intermediate | 241 | 32.80% | 0.00% | 2.07% | 65.15% | NA |
| VI/Aromatic | 96 | 3.10% | 0.00% | 4.17% | 92.71% | NA |
| Intermediate | 90 | 26.70% | 0.00% | 6.67% | 66.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0208664969 | C -> T | LOC_Os02g15470.1 | synonymous_variant ; p.Arg142Arg; LOW | synonymous_codon | Average:4.469; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0208664969 | C -> DEL | LOC_Os02g15470.1 | N | frameshift_variant | Average:4.469; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |