| Variant ID: vg1007671514 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 7671514 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 440. )
GTTTGCTTCACCAGATGAACAGGGAGATGAACCATTATATCAAAGAAAGACAGTGGGAAAAACATCTCCAGGTGACAGAGGGTATTCACAATATCGGTCT[G/A]
CAGCCCATCTAGATCTTCTGGATCTATAACCTTCTGTCCAATTGCATTGAAGAAGGCGCACAGACGTTGGATCGTGTGACGCACTTTCGGTGGTAGAATG
CATTCTACCACCGAAAGTGCGTCACACGATCCAACGTCTGTGCGCCTTCTTCAATGCAATTGGACAGAAGGTTATAGATCCAGAAGATCTAGATGGGCTG[C/T]
AGACCGATATTGTGAATACCCTCTGTCACCTGGAGATGTTTTTCCCACTGTCTTTCTTTGATATAATGGTTCATCTCCCTGTTCATCTGGTGAAGCAAAC
| 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 | 80.60% | 0.30% | 5.23% | 13.86% | NA |
| All Indica | 2759 | 96.50% | 0.20% | 1.49% | 1.85% | NA |
| All Japonica | 1512 | 49.50% | 0.50% | 11.51% | 38.49% | NA |
| Aus | 269 | 92.20% | 0.40% | 7.06% | 0.37% | NA |
| Indica I | 595 | 99.50% | 0.00% | 0.17% | 0.34% | NA |
| Indica II | 465 | 94.60% | 0.00% | 1.51% | 3.87% | NA |
| Indica III | 913 | 97.30% | 0.10% | 1.97% | 0.66% | NA |
| Indica Intermediate | 786 | 94.40% | 0.50% | 1.91% | 3.18% | NA |
| Temperate Japonica | 767 | 56.50% | 0.70% | 9.39% | 33.51% | NA |
| Tropical Japonica | 504 | 29.40% | 0.00% | 14.09% | 56.55% | NA |
| Japonica Intermediate | 241 | 69.30% | 1.20% | 12.86% | 16.60% | NA |
| VI/Aromatic | 96 | 75.00% | 2.10% | 9.38% | 13.54% | NA |
| Intermediate | 90 | 86.70% | 0.00% | 4.44% | 8.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1007671514 | G -> A | LOC_Os10g14130.1 | stop_gained ; p.Gln243*; HIGH | stop_gained | Average:6.761; most accessible tissue: Zhenshan97 flag leaf, score: 12.605 | N | N | N | N |
| vg1007671514 | G -> DEL | LOC_Os10g14130.1 | N | frameshift_variant | Average:6.761; most accessible tissue: Zhenshan97 flag leaf, score: 12.605 | N | N | N | N |