| Variant ID: vg0704649717 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 4649717 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.63, G: 0.37, others allele: 0.00, population size: 254. )
ATATAACACGTCCTCTCTGAAATCGGTGTCTTTGAAGCCTCACCTTGACAATCAACCTCAATGGAATTTCTTGTAGTGTACACAGCCAAATAATTGTAGT[G/A]
CTCCAACTTCAGCTTTAACTTCTGCTTGAGAAGGTGGTTGCTGGGGATGTAAGAGCTTCGTCATCACCACGCTTCCGCTGTCTTGACTCAACCATGGATC
GATCCATGGTTGAGTCAAGACAGCGGAAGCGTGGTGATGACGAAGCTCTTACATCCCCAGCAACCACCTTCTCAAGCAGAAGTTAAAGCTGAAGTTGGAG[C/T]
ACTACAATTATTTGGCTGTGTACACTACAAGAAATTCCATTGAGGTTGATTGTCAAGGTGAGGCTTCAAAGACACCGATTTCAGAGAGGACGTGTTATAT
| 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 | 59.30% | 40.40% | 0.08% | 0.23% | NA |
| All Indica | 2759 | 97.60% | 2.00% | 0.07% | 0.33% | NA |
| All Japonica | 1512 | 0.60% | 99.30% | 0.00% | 0.07% | NA |
| Aus | 269 | 25.30% | 74.70% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.50% | 0.20% | 0.00% | 0.34% | NA |
| Indica II | 465 | 97.00% | 2.80% | 0.22% | 0.00% | NA |
| Indica III | 913 | 98.10% | 1.40% | 0.11% | 0.33% | NA |
| Indica Intermediate | 786 | 95.80% | 3.70% | 0.00% | 0.51% | NA |
| Temperate Japonica | 767 | 0.80% | 99.20% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 0.40% | 99.60% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 0.40% | 99.20% | 0.00% | 0.41% | NA |
| VI/Aromatic | 96 | 2.10% | 97.90% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 36.70% | 60.00% | 2.22% | 1.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0704649717 | G -> DEL | LOC_Os07g08940.1 | N | frameshift_variant | Average:41.44; most accessible tissue: Zhenshan97 young leaf, score: 67.83 | N | N | N | N |
| vg0704649717 | G -> A | LOC_Os07g08940.1 | missense_variant ; p.Ala280Val; MODERATE | nonsynonymous_codon ; A280V | Average:41.44; most accessible tissue: Zhenshan97 young leaf, score: 67.83 | unknown | unknown | TOLERATED | 0.24 |