| Variant ID: vg0817014728 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 17014728 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 268. )
TCAGGACATTGGTACCTCAAACTCCCGAGTGAATGAAGCACCAGACACCAGTTGTGTGGCAGTGGTCCAACACCTGATTAACCAGAACAAATTGCTTATA[G/A]
AGATACTACAGCAGCATCGGATGCCAATTTTGAACCCGAGTCAGATGCAACCTCAAGTGCAGTTGGAGGCAGTCCAAGCACTCACACCACAAGTCAGCGC
GCGCTGACTTGTGGTGTGAGTGCTTGGACTGCCTCCAACTGCACTTGAGGTTGCATCTGACTCGGGTTCAAAATTGGCATCCGATGCTGCTGTAGTATCT[C/T]
TATAAGCAATTTGTTCTGGTTAATCAGGTGTTGGACCACTGCCACACAACTGGTGTCTGGTGCTTCATTCACTCGGGAGTTTGAGGTACCAATGTCCTGA
| 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 | 54.90% | 0.60% | 1.95% | 42.55% | NA |
| All Indica | 2759 | 47.80% | 0.30% | 2.17% | 49.73% | NA |
| All Japonica | 1512 | 67.00% | 0.00% | 0.40% | 32.61% | NA |
| Aus | 269 | 50.60% | 6.70% | 9.29% | 33.46% | NA |
| Indica I | 595 | 26.20% | 0.00% | 1.68% | 72.10% | NA |
| Indica II | 465 | 37.40% | 0.00% | 1.94% | 60.65% | NA |
| Indica III | 913 | 69.00% | 0.30% | 2.85% | 27.82% | NA |
| Indica Intermediate | 786 | 45.70% | 0.60% | 1.91% | 51.78% | NA |
| Temperate Japonica | 767 | 79.80% | 0.00% | 0.00% | 20.21% | NA |
| Tropical Japonica | 504 | 46.60% | 0.00% | 0.99% | 52.38% | NA |
| Japonica Intermediate | 241 | 68.90% | 0.00% | 0.41% | 30.71% | NA |
| VI/Aromatic | 96 | 78.10% | 1.00% | 0.00% | 20.83% | NA |
| Intermediate | 90 | 57.80% | 1.10% | 1.11% | 40.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0817014728 | G -> A | LOC_Os08g27910.1 | missense_variant ; p.Glu46Lys; MODERATE | nonsynonymous_codon ; E46K | Average:5.547; most accessible tissue: Zhenshan97 flower, score: 9.663 | unknown | unknown | DELETERIOUS | 0.01 |
| vg0817014728 | G -> DEL | LOC_Os08g27910.1 | N | frameshift_variant | Average:5.547; most accessible tissue: Zhenshan97 flower, score: 9.663 | N | N | N | N |