| Variant ID: vg0318607903 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 18607903 |
| Reference Allele: A | Alternative Allele: C |
| Primary Allele: A | Secondary Allele: C |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, others allele: 0.00, population size: 277. )
TAACTTCTTTCTTGAAGAGATATCGCATAGAATCGATGGAGCATTTTGCTAGCCTGGCATATTATCTAAAACCATGGAAAGCACTTTTTCTGGTGAAATT[A/C]
TGTCTCAAGTTCCCCATAGCCCTTCCAAATGTAGGAGCGCAGATAAGTAACTAACATTGTCTTGAGTTCTTGACACGCTATATGTTCCACTAAATTCTGT
ACAGAATTTAGTGGAACATATAGCGTGTCAAGAACTCAAGACAATGTTAGTTACTTATCTGCGCTCCTACATTTGGAAGGGCTATGGGGAACTTGAGACA[T/G]
AATTTCACCAGAAAAAGTGCTTTCCATGGTTTTAGATAATATGCCAGGCTAGCAAAATGCTCCATCGATTCTATGCGATATCTCTTCAAGAAAGAAGTTA
| Populations | Population Size | Frequency of A(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 82.40% | 0.70% | 10.05% | 6.88% | NA |
| All Indica | 2759 | 81.70% | 0.20% | 10.95% | 7.18% | NA |
| All Japonica | 1512 | 89.80% | 0.70% | 1.65% | 7.80% | NA |
| Aus | 269 | 49.10% | 0.00% | 49.81% | 1.12% | NA |
| Indica I | 595 | 76.80% | 0.00% | 12.27% | 10.92% | NA |
| Indica II | 465 | 80.40% | 0.00% | 17.63% | 1.94% | NA |
| Indica III | 913 | 88.00% | 0.40% | 5.37% | 6.24% | NA |
| Indica Intermediate | 786 | 78.90% | 0.10% | 12.47% | 8.52% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 73.00% | 2.00% | 3.97% | 21.03% | NA |
| Japonica Intermediate | 241 | 92.50% | 0.40% | 2.07% | 4.98% | NA |
| VI/Aromatic | 96 | 70.80% | 15.60% | 13.54% | 0.00% | NA |
| Intermediate | 90 | 91.10% | 1.10% | 1.11% | 6.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0318607903 | A -> C | LOC_Os03g32540.1 | upstream_gene_variant ; 3290.0bp to feature; MODIFIER | silent_mutation | Average:7.571; most accessible tissue: Zhenshan97 panicle, score: 16.188 | N | N | N | N |
| vg0318607903 | A -> C | LOC_Os03g32526.1 | intron_variant ; MODIFIER | silent_mutation | Average:7.571; most accessible tissue: Zhenshan97 panicle, score: 16.188 | N | N | N | N |
| vg0318607903 | A -> DEL | N | N | silent_mutation | Average:7.571; most accessible tissue: Zhenshan97 panicle, score: 16.188 | N | N | N | N |