| Variant ID: vg1000677878 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 677878 |
| Reference Allele: T | Alternative Allele: G |
| Primary Allele: T | Secondary Allele: G |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 309. )
TTCAGATTTCCAGATCATTTAAAAGTTTATGAAATCTTGAAATGTGCAACAGATCATTTTATAATTGATCAAATATTATCTCTGACGGTTTCCAAGTTTT[T/G]
ACTGTAGACAGTATGAAAATTCGGAACTGACAGAGAGCATATGTTCCCTGAAACATGGGCTGCCACTGTACAGTTTCAGGAAGTACTACAGTGTAGGAAG
CTTCCTACACTGTAGTACTTCCTGAAACTGTACAGTGGCAGCCCATGTTTCAGGGAACATATGCTCTCTGTCAGTTCCGAATTTTCATACTGTCTACAGT[A/C]
AAAACTTGGAAACCGTCAGAGATAATATTTGATCAATTATAAAATGATCTGTTGCACATTTCAAGATTTCATAAACTTTTAAATGATCTGGAAATCTGAA
| Populations | Population Size | Frequency of T(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 97.80% | 2.20% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1000677878 | T -> G | LOC_Os10g02080.1 | downstream_gene_variant ; 2221.0bp to feature; MODIFIER | N | Average:74.974; most accessible tissue: Zhenshan97 young leaf, score: 85.001 | N | N | N | N |
| vg1000677878 | T -> G | LOC_Os10g02070.1 | intron_variant ; MODIFIER | N | Average:74.974; most accessible tissue: Zhenshan97 young leaf, score: 85.001 | N | N | N | N |