| Variant ID: vg0415573913 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 15573913 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, others allele: 0.00, population size: 41. )
CCTTTAACAGCTCAAGGAGTTCTGTAAAATTCTTGTCCGACCAGCCATTACTAGCCTTAAGCTTCATGAGTTCCAACACGCATGACAACTTACTGTGCTT[C/T]
GACTTGCATCCATCATACAACGGCATCTGGCAATCTTCCACCAACTTACTAAACTTCTCATAATCTCTGTCGTTGTCCTCTGCGTCTTCAATGTCATGCA
TGCATGACATTGAAGACGCAGAGGACAACGACAGAGATTATGAGAAGTTTAGTAAGTTGGTGGAAGATTGCCAGATGCCGTTGTATGATGGATGCAAGTC[G/A]
AAGCACAGTAAGTTGTCATGCGTGTTGGAACTCATGAAGCTTAAGGCTAGTAATGGCTGGTCGGACAAGAATTTTACAGAACTCCTTGAGCTGTTAAAGG
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 0.30% | 0.20% | 40.56% | 58.97% | NA |
| All Indica | 2759 | 0.40% | 0.00% | 42.62% | 56.90% | NA |
| All Japonica | 1512 | 0.00% | 0.50% | 42.72% | 56.75% | NA |
| Aus | 269 | 0.00% | 0.00% | 3.35% | 96.65% | NA |
| Indica I | 595 | 0.50% | 0.00% | 32.44% | 67.06% | NA |
| Indica II | 465 | 1.70% | 0.00% | 35.27% | 63.01% | NA |
| Indica III | 913 | 0.00% | 0.00% | 56.19% | 43.81% | NA |
| Indica Intermediate | 786 | 0.10% | 0.10% | 38.93% | 60.81% | NA |
| Temperate Japonica | 767 | 0.00% | 0.90% | 27.90% | 71.19% | NA |
| Tropical Japonica | 504 | 0.00% | 0.00% | 60.91% | 39.09% | NA |
| Japonica Intermediate | 241 | 0.00% | 0.40% | 51.87% | 47.72% | NA |
| VI/Aromatic | 96 | 0.00% | 0.00% | 46.88% | 53.12% | NA |
| Intermediate | 90 | 0.00% | 1.10% | 45.56% | 53.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0415573913 | C -> DEL | LOC_Os04g26690.1 | N | frameshift_variant | Average:9.21; most accessible tissue: Minghui63 root, score: 21.615 | N | N | N | N |
| vg0415573913 | C -> T | LOC_Os04g26690.1 | synonymous_variant ; p.Ser215Ser; LOW | synonymous_codon | Average:9.21; most accessible tissue: Minghui63 root, score: 21.615 | N | N | N | N |