| Variant ID: vg0114587683 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 14587683 |
| Reference Allele: G | Alternative Allele: C |
| Primary Allele: G | Secondary Allele: C |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 254. )
TCCACATTTGGAGGGAAAATGAAAATTGAGACAGTACCGAGTAGATATCTCCATATATTTGTACCTCTGAAGAGAACAATCCCTGATACAAATTACTGAT[G/C]
CAAAAATAAGTTGTTTTCGGCCCCCATAGACATTATGAAATTCCTCTTGACTTGAATACAGAAAGGATTCAATCATGCACTACCTTTTGTACAGGGAGTA
TACTCCCTGTACAAAAGGTAGTGCATGATTGAATCCTTTCTGTATTCAAGTCAAGAGGAATTTCATAATGTCTATGGGGGCCGAAAACAACTTATTTTTG[C/G]
ATCAGTAATTTGTATCAGGGATTGTTCTCTTCAGAGGTACAAATATATGGAGATATCTACTCGGTACTGTCTCAATTTTCATTTTCCCTCCAAATGTGGA
| Populations | Population Size | Frequency of G(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 81.20% | 2.10% | 0.23% | 16.46% | NA |
| All Indica | 2759 | 68.20% | 3.50% | 0.40% | 27.87% | 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 | 52.10% | 0.00% | 0.34% | 47.56% | NA |
| Indica II | 465 | 59.80% | 14.00% | 0.65% | 25.59% | NA |
| Indica III | 913 | 80.70% | 0.20% | 0.22% | 18.84% | NA |
| Indica Intermediate | 786 | 70.90% | 3.80% | 0.51% | 24.81% | 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 | 91.10% | 1.10% | 0.00% | 7.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0114587683 | G -> DEL | N | N | silent_mutation | Average:67.085; most accessible tissue: Zhenshan97 young leaf, score: 80.589 | N | N | N | N |
| vg0114587683 | G -> C | LOC_Os01g25730.1 | downstream_gene_variant ; 4305.0bp to feature; MODIFIER | silent_mutation | Average:67.085; most accessible tissue: Zhenshan97 young leaf, score: 80.589 | N | N | N | N |
| vg0114587683 | G -> C | LOC_Os01g25740.1 | intron_variant ; MODIFIER | silent_mutation | Average:67.085; most accessible tissue: Zhenshan97 young leaf, score: 80.589 | N | N | N | N |