| Variant ID: vg0114587493 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr01 | Position: 14587493 |
| Reference Allele: C | Alternative Allele: CAA |
| Primary Allele: C | Secondary Allele: CAA |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 263. )
TTTTTTTTTATTGCTGAAGAGTACATTAATTTAAGTGTTGCATTCATGGTAAGAACAAGAACAACTATACAGAGTTTTTGTATGTACGAAGTTGAGTACT[C/CAA]
ACATATGTCAACGTCATTTACCTAGACAAATTTGAAGAATTCAGCAGAAGAAAGATTATGTTCTTGGTTTTCCATAGTCCACATCATGGTCCACATTTGG
CCAAATGTGGACCATGATGTGGACTATGGAAAACCAAGAACATAATCTTTCTTCTGCTGAATTCTTCAAATTTGTCTAGGTAAATGACGTTGACATATGT[G/TTG]
AGTACTCAACTTCGTACATACAAAAACTCTGTATAGTTGTTCTTGTTCTTACCATGAATGCAACACTTAAATTAATGTACTCTTCAGCAATAAAAAAAAA
| Populations | Population Size | Frequency of C(primary allele) | Frequency of CAA(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 77.90% | 2.10% | 0.32% | 19.72% | NA |
| All Indica | 2759 | 62.70% | 3.50% | 0.54% | 33.31% | NA |
| All Japonica | 1512 | 99.90% | 0.00% | 0.00% | 0.13% | NA |
| Aus | 269 | 99.30% | 0.70% | 0.00% | 0.00% | NA |
| Indica I | 595 | 52.40% | 0.00% | 0.50% | 47.06% | NA |
| Indica II | 465 | 57.40% | 14.00% | 0.22% | 28.39% | NA |
| Indica III | 913 | 70.00% | 0.20% | 0.44% | 29.35% | NA |
| Indica Intermediate | 786 | 65.00% | 3.70% | 0.89% | 30.41% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.80% | 0.00% | 0.00% | 0.20% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.00% | 0.00% | 0.41% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 86.70% | 1.10% | 0.00% | 12.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0114587493 | C -> DEL | N | N | silent_mutation | Average:62.395; most accessible tissue: Zhenshan97 young leaf, score: 77.101 | N | N | N | N |
| vg0114587493 | C -> CAA | LOC_Os01g25730.1 | downstream_gene_variant ; 4116.0bp to feature; MODIFIER | silent_mutation | Average:62.395; most accessible tissue: Zhenshan97 young leaf, score: 77.101 | N | N | N | N |
| vg0114587493 | C -> CAA | LOC_Os01g25740.1 | intron_variant ; MODIFIER | silent_mutation | Average:62.395; most accessible tissue: Zhenshan97 young leaf, score: 77.101 | N | N | N | N |