| Variant ID: vg0402803488 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 2803488 |
| Reference Allele: A | Alternative Allele: C |
| Primary Allele: A | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
AACTAGCTAGTTCTGAATATTTGTTCTGCTTCAAGCACAACATCTCCATGTGTTCTGAACTTAAATACTGAGATTCCTGAAGAACAGATTCTGGAAGACG[A/C]
GTGCATTCCATCTGAATACGCGGTTTGCAGACGTCGGCTCGGTGACGACACATGAGTCAGAAGCAAATCAGGATTCGATAACGTTCATGCTTTCCTTGAC
GTCAAGGAAAGCATGAACGTTATCGAATCCTGATTTGCTTCTGACTCATGTGTCGTCACCGAGCCGACGTCTGCAAACCGCGTATTCAGATGGAATGCAC[T/G]
CGTCTTCCAGAATCTGTTCTTCAGGAATCTCAGTATTTAAGTTCAGAACACATGGAGATGTTGTGCTTGAAGCAGAACAAATATTCAGAACTAGCTAGTT
| 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 | 22.80% | 4.30% | 9.78% | 63.16% | NA |
| All Indica | 2759 | 8.80% | 0.40% | 10.84% | 79.92% | NA |
| All Japonica | 1512 | 43.50% | 11.40% | 8.07% | 36.97% | NA |
| Aus | 269 | 39.40% | 5.90% | 12.64% | 42.01% | NA |
| Indica I | 595 | 4.50% | 0.00% | 3.36% | 92.10% | NA |
| Indica II | 465 | 11.00% | 0.20% | 1.51% | 87.31% | NA |
| Indica III | 913 | 9.90% | 0.40% | 20.92% | 68.78% | NA |
| Indica Intermediate | 786 | 9.70% | 0.80% | 10.31% | 79.26% | NA |
| Temperate Japonica | 767 | 78.20% | 9.90% | 1.56% | 10.30% | NA |
| Tropical Japonica | 504 | 3.80% | 6.20% | 11.51% | 78.57% | NA |
| Japonica Intermediate | 241 | 16.20% | 27.40% | 21.58% | 34.85% | NA |
| VI/Aromatic | 96 | 44.80% | 0.00% | 0.00% | 55.21% | NA |
| Intermediate | 90 | 27.80% | 3.30% | 7.78% | 61.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0402803488 | A -> C | LOC_Os04g05550.1 | upstream_gene_variant ; 521.0bp to feature; MODIFIER | silent_mutation | Average:10.149; most accessible tissue: Callus, score: 41.457 | N | N | N | N |
| vg0402803488 | A -> C | LOC_Os04g05540.1 | downstream_gene_variant ; 2151.0bp to feature; MODIFIER | silent_mutation | Average:10.149; most accessible tissue: Callus, score: 41.457 | N | N | N | N |
| vg0402803488 | A -> C | LOC_Os04g05550-LOC_Os04g05560 | intergenic_region ; MODIFIER | silent_mutation | Average:10.149; most accessible tissue: Callus, score: 41.457 | N | N | N | N |
| vg0402803488 | A -> DEL | N | N | silent_mutation | Average:10.149; most accessible tissue: Callus, score: 41.457 | N | N | N | N |