| Variant ID: vg0508168878 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 8168878 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, others allele: 0.00, population size: 304. )
CACCGACTCCTCCTCGTGCTCCTACACCTACTCCCCCGCAAGCTCCTCTTCCGGCACCTTCAAAGTCAAGGGCCCCCCCAGCTCCACCGCCTGCCCACAC[A/G]
AGGGCAACGAAGAAGGCGAAAGTTGACGCCACCAAGAACAAGGACCCGGGGTACGATTGCACGCAAGAGGAGCTTGACGCTTACGTTGCATCAGAAGTCA
TGACTTCTGATGCAACGTAAGCGTCAAGCTCCTCTTGCGTGCAATCGTACCCCGGGTCCTTGTTCTTGGTGGCGTCAACTTTCGCCTTCTTCGTTGCCCT[T/C]
GTGTGGGCAGGCGGTGGAGCTGGGGGGGCCCTTGACTTTGAAGGTGCCGGAAGAGGAGCTTGCGGGGGAGTAGGTGTAGGAGCACGAGGAGGAGTCGGTG
| 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 | 51.80% | 0.20% | 17.69% | 30.34% | NA |
| All Indica | 2759 | 29.30% | 0.30% | 27.33% | 43.06% | NA |
| All Japonica | 1512 | 93.00% | 0.00% | 0.26% | 6.75% | NA |
| Aus | 269 | 26.40% | 0.00% | 26.39% | 47.21% | NA |
| Indica I | 595 | 35.80% | 0.50% | 13.45% | 50.25% | NA |
| Indica II | 465 | 33.50% | 0.00% | 19.78% | 46.67% | NA |
| Indica III | 913 | 20.30% | 0.00% | 43.59% | 36.14% | NA |
| Indica Intermediate | 786 | 32.40% | 0.60% | 23.41% | 43.51% | NA |
| Temperate Japonica | 767 | 91.70% | 0.00% | 0.00% | 8.34% | NA |
| Tropical Japonica | 504 | 98.60% | 0.00% | 0.60% | 0.79% | NA |
| Japonica Intermediate | 241 | 85.50% | 0.00% | 0.41% | 14.11% | NA |
| VI/Aromatic | 96 | 99.00% | 0.00% | 0.00% | 1.04% | NA |
| Intermediate | 90 | 74.40% | 0.00% | 7.78% | 17.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0508168878 | A -> DEL | LOC_Os05g14460.1 | N | frameshift_variant | Average:10.758; most accessible tissue: Zhenshan97 flag leaf, score: 18.298 | N | N | N | N |
| vg0508168878 | A -> G | LOC_Os05g14460.1 | synonymous_variant ; p.Thr624Thr; LOW | synonymous_codon | Average:10.758; most accessible tissue: Zhenshan97 flag leaf, score: 18.298 | N | N | N | N |