| Variant ID: vg0424400607 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 24400607 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 354. )
TCGTACACAATGTGATTGGGCTCGCAACCAGAAGATAACATAGCATCTAGTAATTCATGAGCATGGTCCACTTTGTGAGCTTTGCATAAACCATCTACTA[G/A]
TGCACCATATGTCACAACATTTGGAGCAAGTGTGTGTCTGTCCTCACATGGAAAGTAAAAATCAGAATCGGCGCTATCAGAAGTTCCAATTAATTTGGCA
TGCCAAATTAATTGGAACTTCTGATAGCGCCGATTCTGATTTTTACTTTCCATGTGAGGACAGACACACACTTGCTCCAAATGTTGTGACATATGGTGCA[C/T]
TAGTAGATGGTTTATGCAAAGCTCACAAAGTGGACCATGCTCATGAATTACTAGATGCTATGTTATCTTCTGGTTGCGAGCCCAATCACATTGTGTACGA
| 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 | 96.00% | 4.00% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 96.00% | 4.00% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Aus | 269 | 72.50% | 27.50% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 99.10% | 0.90% | 0.00% | 0.00% | NA |
| Indica III | 913 | 92.70% | 7.30% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 94.90% | 5.10% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 95.60% | 4.40% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0424400607 | G -> A | LOC_Os04g41140.1 | synonymous_variant ; p.Leu619Leu; LOW | synonymous_codon | Average:51.227; most accessible tissue: Zhenshan97 young leaf, score: 84.431 | N | N | N | N |