| Variant ID: vg1000677783 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 677783 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 250. )
GGGTCGGCTGAGCTTGAGGTGGTCGACAACCGGTTGCTGAACAGCGTGCACCGGGCTCGTCCGATCGTGTGCCCTCCTATTGATGATCAATGAGTTTCAG[A/G]
TTTCCAGATCATTTAAAAGTTTATGAAATCTTGAAATGTGCAACAGATCATTTTATAATTGATCAAATATTATCTCTGACGGTTTCCAAGTTTTTACTGT
ACAGTAAAAACTTGGAAACCGTCAGAGATAATATTTGATCAATTATAAAATGATCTGTTGCACATTTCAAGATTTCATAAACTTTTAAATGATCTGGAAA[T/C]
CTGAAACTCATTGATCATCAATAGGAGGGCACACGATCGGACGAGCCCGGTGCACGCTGTTCAGCAACCGGTTGTCGACCACCTCAAGCTCAGCCGACCC
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 98.10% | 1.90% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| Aus | 269 | 96.70% | 3.30% | 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 | 97.20% | 2.80% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.70% | 0.30% | 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 | 97.90% | 2.10% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 56.20% | 43.80% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 92.20% | 7.80% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1000677783 | A -> G | LOC_Os10g02080.1 | downstream_gene_variant ; 2316.0bp to feature; MODIFIER | silent_mutation | Average:77.356; most accessible tissue: Zhenshan97 young leaf, score: 86.055 | N | N | N | N |
| vg1000677783 | A -> G | LOC_Os10g02070.1 | intron_variant ; MODIFIER | silent_mutation | Average:77.356; most accessible tissue: Zhenshan97 young leaf, score: 86.055 | N | N | N | N |