| Variant ID: vg1000678603 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 678603 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.02, others allele: 0.00, population size: 291. )
CACCCCTGAAATGCACAACAAATTTTCAGTAATTGTGACACAACTAGTCAATTTAATATGTATGTAGAACATTCAGATAAAGTTCAGAGATGTGTGAAAA[G/A]
GGTAGTTAATGTATACATTGACAAAGCAGTCATGGAAATGGAGCCTTAGGAGGGAGGCACCCATCCTCATCTCAGTCCTCATGGCAGCATAAACATGCTG
CAGCATGTTTATGCTGCCATGAGGACTGAGATGAGGATGGGTGCCTCCCTCCTAAGGCTCCATTTCCATGACTGCTTTGTCAATGTATACATTAACTACC[C/T]
TTTTCACACATCTCTGAACTTTATCTGAATGTTCTACATACATATTAAATTGACTAGTTGTGTCACAATTACTGAAAATTTGTTGTGCATTTCAGGGGTG
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 97.40% | 2.60% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 97.90% | 2.10% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Aus | 269 | 79.60% | 20.40% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 99.40% | 0.60% | 0.00% | 0.00% | NA |
| Indica III | 913 | 97.60% | 2.40% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 95.80% | 4.20% | 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 | 99.20% | 0.80% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 97.90% | 2.10% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 95.60% | 4.40% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1000678603 | G -> A | LOC_Os10g02080.1 | downstream_gene_variant ; 1496.0bp to feature; MODIFIER | silent_mutation | Average:72.074; most accessible tissue: Minghui63 root, score: 87.125 | N | N | N | N |
| vg1000678603 | G -> A | LOC_Os10g02070.1 | intron_variant ; MODIFIER | silent_mutation | Average:72.074; most accessible tissue: Minghui63 root, score: 87.125 | N | N | N | N |