| Variant ID: vg0721994365 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 21994365 |
| Reference Allele: C | Alternative Allele: G |
| Primary Allele: C | Secondary Allele: G |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 309. )
ATTGGCCCAGATCCTTGACCTCAAACTCCTTGCTTAGATTTTGTTTCAACCTAGATATCTCCAAGCAATCATCTCCAGTGATAATCATGTCATCAACATA[C/G]
ACAACAAGAATAGTTTTAAGACCTCTATTATGGCGATAGAAAACTGTGTGGTCTCCATTGCACTGTTTATAACCCATACCACACATTGCACGTCTAAAGC
GCTTTAGACGTGCAATGTGTGGTATGGGTTATAAACAGTGCAATGGAGACCACACAGTTTTCTATCGCCATAATAGAGGTCTTAAAACTATTCTTGTTGT[G/C]
TATGTTGATGACATGATTATCACTGGAGATGATTGCTTGGAGATATCTAGGTTGAAACAAAATCTAAGCAAGGAGTTTGAGGTCAAGGATCTGGGCCAAT
| Populations | Population Size | Frequency of C(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 79.30% | 0.10% | 8.34% | 12.21% | NA |
| All Indica | 2759 | 81.20% | 0.00% | 2.46% | 16.38% | NA |
| All Japonica | 1512 | 79.70% | 0.50% | 12.17% | 7.67% | NA |
| Aus | 269 | 49.40% | 0.00% | 49.44% | 1.12% | NA |
| Indica I | 595 | 42.20% | 0.00% | 3.53% | 54.29% | NA |
| Indica II | 465 | 92.00% | 0.00% | 1.94% | 6.02% | NA |
| Indica III | 913 | 99.60% | 0.00% | 0.44% | 0.00% | NA |
| Indica Intermediate | 786 | 82.80% | 0.00% | 4.33% | 12.85% | NA |
| Temperate Japonica | 767 | 90.90% | 0.90% | 5.08% | 3.13% | NA |
| Tropical Japonica | 504 | 67.90% | 0.00% | 21.63% | 10.52% | NA |
| Japonica Intermediate | 241 | 68.90% | 0.00% | 14.94% | 16.18% | NA |
| VI/Aromatic | 96 | 99.00% | 0.00% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 84.40% | 0.00% | 8.89% | 6.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0721994365 | C -> DEL | LOC_Os07g36710.1 | N | frameshift_variant | Average:4.565; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0721994365 | C -> G | LOC_Os07g36710.1 | synonymous_variant ; p.Val486Val; LOW | synonymous_codon | Average:4.565; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |