| Variant ID: vg0904847583 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 4847583 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.01, others allele: 0.00, population size: 195. )
GACCCATTCCTTGACAATTGAAGCAACAGATATCTTCCCGGACTCGGCATTTTCTTTTCTCATTTTGATTCCTCTGTCCTGGCACTGGAGTTAGGCTGAA[A/G]
CTGGAATCTTGGCGAGGATTTGTGTTTCCTTGATGCTTCCCTCCGTTGGAACTGGCGGGTTGGTTGGCCATCTTCTTCGTCAGCAGAAAACTGAATCGAC
GTCGATTCAGTTTTCTGCTGACGAAGAAGATGGCCAACCAACCCGCCAGTTCCAACGGAGGGAAGCATCAAGGAAACACAAATCCTCGCCAAGATTCCAG[T/C]
TTCAGCCTAACTCCAGTGCCAGGACAGAGGAATCAAAATGAGAAAAGAAAATGCCGAGTCCGGGAAGATATCTGTTGCTTCAATTGTCAAGGAATGGGTC
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 17.30% | 1.60% | 4.15% | 77.00% | NA |
| All Indica | 2759 | 4.50% | 0.00% | 2.90% | 92.57% | NA |
| All Japonica | 1512 | 35.50% | 4.80% | 6.15% | 53.57% | NA |
| Aus | 269 | 18.20% | 0.00% | 5.58% | 76.21% | NA |
| Indica I | 595 | 6.20% | 0.00% | 1.51% | 92.27% | NA |
| Indica II | 465 | 5.80% | 0.00% | 1.08% | 93.12% | NA |
| Indica III | 913 | 1.90% | 0.00% | 2.52% | 95.62% | NA |
| Indica Intermediate | 786 | 5.60% | 0.00% | 5.47% | 88.93% | NA |
| Temperate Japonica | 767 | 46.20% | 0.50% | 2.48% | 50.85% | NA |
| Tropical Japonica | 504 | 21.60% | 4.00% | 8.33% | 66.07% | NA |
| Japonica Intermediate | 241 | 30.70% | 19.90% | 13.28% | 36.10% | NA |
| VI/Aromatic | 96 | 83.30% | 0.00% | 2.08% | 14.58% | NA |
| Intermediate | 90 | 28.90% | 2.20% | 6.67% | 62.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0904847583 | A -> G | LOC_Os09g09070.1 | synonymous_variant ; p.Ser285Ser; LOW | synonymous_codon | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0904847583 | A -> DEL | LOC_Os09g09070.1 | N | frameshift_variant | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |