| Variant ID: vg0404363081 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 4363081 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 309. )
CTACATGTTCCTTGAACACGTTGGGTGGTAGGCCTTTCGTGAGCGGATCCGCGAGCATCCTTTCTGTTTTAATGTGCTCGAGACTGATTGTTTGATCCCG[G/T]
ACTTTGTCCTTCACAACATAGTACTTTATGTCAATGTGTTTGGCAGCACCACTTGACTGATTGTTGTGAGCGTACATTACTGCGGGTTCGTTGTCGCAGT
ACTGCGACAACGAACCCGCAGTAATGTACGCTCACAACAATCAGTCAAGTGGTGCTGCCAAACACATTGACATAAAGTACTATGTTGTGAAGGACAAAGT[C/A]
CGGGATCAAACAATCAGTCTCGAGCACATTAAAACAGAAAGGATGCTCGCGGATCCGCTCACGAAAGGCCTACCACCCAACGTGTTCAAGGAACATGTAG
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 8.70% | 0.70% | 23.95% | 66.65% | NA |
| All Indica | 2759 | 9.80% | 0.20% | 20.70% | 69.30% | NA |
| All Japonica | 1512 | 7.80% | 1.70% | 32.21% | 58.27% | NA |
| Aus | 269 | 5.90% | 0.00% | 13.75% | 80.30% | NA |
| Indica I | 595 | 8.20% | 0.00% | 24.54% | 67.23% | NA |
| Indica II | 465 | 20.20% | 0.20% | 25.59% | 53.98% | NA |
| Indica III | 913 | 3.40% | 0.00% | 15.88% | 80.72% | NA |
| Indica Intermediate | 786 | 12.30% | 0.50% | 20.48% | 66.67% | NA |
| Temperate Japonica | 767 | 12.60% | 2.70% | 53.72% | 30.90% | NA |
| Tropical Japonica | 504 | 3.00% | 1.00% | 4.56% | 91.47% | NA |
| Japonica Intermediate | 241 | 2.50% | 0.00% | 21.58% | 75.93% | NA |
| VI/Aromatic | 96 | 0.00% | 0.00% | 13.54% | 86.46% | NA |
| Intermediate | 90 | 8.90% | 0.00% | 26.67% | 64.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0404363081 | G -> DEL | LOC_Os04g08210.1 | N | frameshift_variant | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0404363081 | G -> T | LOC_Os04g08210.1 | synonymous_variant ; p.Val1363Val; LOW | synonymous_codon | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |