| Variant ID: vg0208664984 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 8664984 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 336. )
CGTACGAGGCTAAGAAGATAGTCTGCCCGTTAGGACTGGAAGTTCATAAGATTCACGCATGTCCGAACGATTGTATCCTATATCGCGGTGAGGAGTATGA[G/A]
AACCTAGAAGCATGCCCTGTTTGCAAAGCACTACGATACAAGATTAGACGGGACGATCCAGGAGAAGTTGACGGGCAGCTAACAAAGAAGAGAATTCCTG
CAGGAATTCTCTTCTTTGTTAGCTGCCCGTCAACTTCTCCTGGATCGTCCCGTCTAATCTTGTATCGTAGTGCTTTGCAAACAGGGCATGCTTCTAGGTT[C/T]
TCATACTCCTCACCGCGATATAGGATACAATCGTTCGGACATGCGTGAATCTTATGAACTTCCAGTCCTAACGGGCAGACTATCTTCTTAGCCTCGTACG
| 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 | 24.30% | 0.10% | 7.24% | 68.32% | NA |
| All Indica | 2759 | 12.30% | 0.00% | 10.26% | 77.42% | NA |
| All Japonica | 1512 | 50.90% | 0.50% | 2.71% | 45.97% | NA |
| Aus | 269 | 4.80% | 0.00% | 2.60% | 92.57% | NA |
| Indica I | 595 | 12.80% | 0.00% | 10.08% | 77.14% | NA |
| Indica II | 465 | 8.80% | 0.00% | 10.54% | 80.65% | NA |
| Indica III | 913 | 12.70% | 0.00% | 10.41% | 76.89% | NA |
| Indica Intermediate | 786 | 13.60% | 0.00% | 10.05% | 76.34% | NA |
| Temperate Japonica | 767 | 77.30% | 0.10% | 1.96% | 20.60% | NA |
| Tropical Japonica | 504 | 19.40% | 1.20% | 3.97% | 75.40% | NA |
| Japonica Intermediate | 241 | 32.40% | 0.00% | 2.49% | 65.15% | NA |
| VI/Aromatic | 96 | 2.10% | 0.00% | 5.21% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0208664984 | G -> A | LOC_Os02g15470.1 | synonymous_variant ; p.Glu147Glu; LOW | synonymous_codon | Average:4.469; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0208664984 | G -> DEL | LOC_Os02g15470.1 | N | frameshift_variant | Average:4.469; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |