| Variant ID: vg0704650412 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 4650412 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.95, A: 0.06, others allele: 0.00, population size: 213. )
GTGTTGCAATAGCAGCTGCGGTAGTTGAGGGTGTGGATGAGTTCATAGTGGCTGGAAACACATGTTCTGGTGCAGCAAGAGAACTCTCAACTGCTGGCCT[A/G]
GTGGTGATGCTGCTTGGTCCCAACGTCAAACACTTGGTGGGCGTCATGTCGACACCGTTCCCGTTGAAAGGATGCACGTGCTGGACATCAAGCAGGTAAC
GTTACCTGCTTGATGTCCAGCACGTGCATCCTTTCAACGGGAACGGTGTCGACATGACGCCCACCAAGTGTTTGACGTTGGGACCAAGCAGCATCACCAC[T/C]
AGGCCAGCAGTTGAGAGTTCTCTTGCTGCACCAGAACATGTGTTTCCAGCCACTATGAACTCATCCACACCCTCAACTACCGCAGCTGCTATTGCAACAC
| 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 | 59.30% | 40.40% | 0.08% | 0.28% | NA |
| All Indica | 2759 | 97.60% | 2.00% | 0.00% | 0.40% | NA |
| All Japonica | 1512 | 0.50% | 99.40% | 0.07% | 0.07% | NA |
| Aus | 269 | 25.70% | 74.30% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.50% | 0.20% | 0.00% | 0.34% | NA |
| Indica II | 465 | 97.00% | 2.80% | 0.00% | 0.22% | NA |
| Indica III | 913 | 98.10% | 1.40% | 0.00% | 0.44% | NA |
| Indica Intermediate | 786 | 95.90% | 3.60% | 0.00% | 0.51% | NA |
| Temperate Japonica | 767 | 0.50% | 99.30% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 0.40% | 99.60% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 0.40% | 99.20% | 0.00% | 0.41% | NA |
| VI/Aromatic | 96 | 1.00% | 99.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 35.60% | 60.00% | 3.33% | 1.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0704650412 | A -> DEL | LOC_Os07g08940.1 | N | frameshift_variant | Average:56.15; most accessible tissue: Zhenshan97 young leaf, score: 76.44 | N | N | N | N |
| vg0704650412 | A -> G | LOC_Os07g08940.1 | synonymous_variant ; p.Thr48Thr; LOW | synonymous_codon | Average:56.15; most accessible tissue: Zhenshan97 young leaf, score: 76.44 | N | N | N | N |