| Variant ID: vg1007671530 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 7671530 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 427. )
GAACAGGGAGATGAACCATTATATCAAAGAAAGACAGTGGGAAAAACATCTCCAGGTGACAGAGGGTATTCACAATATCGGTCTGCAGCCCATCTAGATC[T/C]
TCTGGATCTATAACCTTCTGTCCAATTGCATTGAAGAAGGCGCACAGACGTTGGATCGTGTGACGCACTTTCGGTGGTAGAATGCCTCTGATAGCAACTG
CAGTTGCTATCAGAGGCATTCTACCACCGAAAGTGCGTCACACGATCCAACGTCTGTGCGCCTTCTTCAATGCAATTGGACAGAAGGTTATAGATCCAGA[A/G]
GATCTAGATGGGCTGCAGACCGATATTGTGAATACCCTCTGTCACCTGGAGATGTTTTTCCCACTGTCTTTCTTTGATATAATGGTTCATCTCCCTGTTC
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 14.90% | 0.50% | 19.89% | 64.75% | NA |
| All Indica | 2759 | 3.70% | 0.80% | 20.51% | 74.99% | NA |
| All Japonica | 1512 | 38.40% | 0.00% | 7.87% | 53.77% | NA |
| Aus | 269 | 0.70% | 0.00% | 72.49% | 26.77% | NA |
| Indica I | 595 | 1.00% | 0.30% | 4.37% | 94.29% | NA |
| Indica II | 465 | 2.60% | 0.60% | 27.31% | 69.46% | NA |
| Indica III | 913 | 5.50% | 1.40% | 25.63% | 67.47% | NA |
| Indica Intermediate | 786 | 4.20% | 0.60% | 22.77% | 72.39% | NA |
| Temperate Japonica | 767 | 53.20% | 0.00% | 6.65% | 40.16% | NA |
| Tropical Japonica | 504 | 8.70% | 0.00% | 9.52% | 81.75% | NA |
| Japonica Intermediate | 241 | 53.10% | 0.00% | 8.30% | 38.59% | NA |
| VI/Aromatic | 96 | 8.30% | 0.00% | 41.67% | 50.00% | NA |
| Intermediate | 90 | 13.30% | 0.00% | 22.22% | 64.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1007671530 | T -> C | LOC_Os10g14130.1 | synonymous_variant ; p.Glu237Glu; LOW | synonymous_codon | Average:6.521; most accessible tissue: Zhenshan97 flag leaf, score: 10.769 | N | N | N | N |
| vg1007671530 | T -> DEL | LOC_Os10g14130.1 | N | frameshift_variant | Average:6.521; most accessible tissue: Zhenshan97 flag leaf, score: 10.769 | N | N | N | N |