| Variant ID: vg0335310117 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 35310117 |
| Reference Allele: C | Alternative Allele: A,T |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 69. )
ACAAATCGACCTTTAATAAAATTTATTTTGAAAATAGACCCAAAATATTCCTTACTTCCCTAAATGTTTGACGCTGTTGACTTTTTAAAGTATGTTTAAC[C/A,T]
ATTTGTCTTATTCAAAAACTTTTGTGAAATATGTAAAACTATATGTATATATAAAAGTATATTTAACAATAAATCAAATGATAGGAAAAGAATTAATTAT
ATAATTAATTCTTTTCCTATCATTTGATTTATTGTTAAATATACTTTTATATATACATATAGTTTTACATATTTCACAAAAGTTTTTGAATAAGACAAAT[G/T,A]
GTTAAACATACTTTAAAAAGTCAACAGCGTCAAACATTTAGGGAAGTAAGGAATATTTTGGGTCTATTTTCAAAATAAATTTTATTAAAGGTCGATTTGT
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 81.40% | 17.50% | 0.11% | 0.00% | T: 0.93% |
| All Indica | 2759 | 69.20% | 29.10% | 0.11% | 0.00% | T: 1.52% |
| All Japonica | 1512 | 99.60% | 0.30% | 0.07% | 0.00% | T: 0.07% |
| Aus | 269 | 99.60% | 0.00% | 0.00% | 0.00% | T: 0.37% |
| Indica I | 595 | 77.10% | 18.30% | 0.00% | 0.00% | T: 4.54% |
| Indica II | 465 | 43.70% | 55.70% | 0.43% | 0.00% | T: 0.22% |
| Indica III | 913 | 83.90% | 15.80% | 0.11% | 0.00% | T: 0.22% |
| Indica Intermediate | 786 | 61.30% | 37.20% | 0.00% | 0.00% | T: 1.53% |
| Temperate Japonica | 767 | 99.60% | 0.30% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.00% | 0.00% | 0.00% | T: 0.41% |
| VI/Aromatic | 96 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 77.80% | 21.10% | 1.11% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0335310117 | C -> T | LOC_Os03g62330.1 | 3_prime_UTR_variant ; 192.0bp to feature; MODIFIER | silent_mutation | Average:59.444; most accessible tissue: Minghui63 root, score: 79.74 | N | N | N | N |
| vg0335310117 | C -> T | LOC_Os03g62314.1 | upstream_gene_variant ; 731.0bp to feature; MODIFIER | silent_mutation | Average:59.444; most accessible tissue: Minghui63 root, score: 79.74 | N | N | N | N |
| vg0335310117 | C -> T | LOC_Os03g62340.1 | downstream_gene_variant ; 2334.0bp to feature; MODIFIER | silent_mutation | Average:59.444; most accessible tissue: Minghui63 root, score: 79.74 | N | N | N | N |
| vg0335310117 | C -> A | LOC_Os03g62330.1 | 3_prime_UTR_variant ; 192.0bp to feature; MODIFIER | silent_mutation | Average:59.444; most accessible tissue: Minghui63 root, score: 79.74 | N | N | N | N |
| vg0335310117 | C -> A | LOC_Os03g62314.1 | upstream_gene_variant ; 731.0bp to feature; MODIFIER | silent_mutation | Average:59.444; most accessible tissue: Minghui63 root, score: 79.74 | N | N | N | N |
| vg0335310117 | C -> A | LOC_Os03g62340.1 | downstream_gene_variant ; 2334.0bp to feature; MODIFIER | silent_mutation | Average:59.444; most accessible tissue: Minghui63 root, score: 79.74 | N | N | N | N |