| Variant ID: vg0334134018 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 34134018 |
| 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: 359. )
AGGCCGACCACCGTACGAAGCCTAAACATCGCAGCGGGAAAACAGTGTTTGCTATGGTTAAAGATCTTAAAGTAGTGTTCGGAAAGGGGCCTGGAAGCCA[G/A]
CATATAGAGAGCGAAGATGGTCACGCGGCGATGTGGAAAAAGAACTCTATATTTTGGGAGTTACCATATTGGGAATTCTTGGACGTACGCCACGCAATCG
CGATTGCGTGGCGTACGTCCAAGAATTCCCAATATGGTAACTCCCAAAATATAGAGTTCTTTTTCCACATCGCCGCGTGACCATCTTCGCTCTCTATATG[C/T]
TGGCTTCCAGGCCCCTTTCCGAACACTACTTTAAGATCTTTAACCATAGCAAACACTGTTTTCCCGCTGCGATGTTTAGGCTTCGTACGGTGGTCGGCCT
| 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 | 0.60% | 0.30% | 17.90% | 81.15% | NA |
| All Indica | 2759 | 0.60% | 0.30% | 18.77% | 80.36% | NA |
| All Japonica | 1512 | 0.40% | 0.10% | 13.29% | 86.24% | NA |
| Aus | 269 | 2.20% | 3.00% | 38.29% | 56.51% | NA |
| Indica I | 595 | 0.30% | 0.30% | 6.72% | 92.61% | NA |
| Indica II | 465 | 0.40% | 0.20% | 10.75% | 88.60% | NA |
| Indica III | 913 | 0.50% | 0.20% | 32.53% | 66.70% | NA |
| Indica Intermediate | 786 | 1.00% | 0.30% | 16.67% | 82.06% | NA |
| Temperate Japonica | 767 | 0.40% | 0.00% | 3.78% | 95.83% | NA |
| Tropical Japonica | 504 | 0.60% | 0.20% | 27.98% | 71.23% | NA |
| Japonica Intermediate | 241 | 0.00% | 0.00% | 12.86% | 87.14% | NA |
| VI/Aromatic | 96 | 0.00% | 0.00% | 5.21% | 94.79% | NA |
| Intermediate | 90 | 0.00% | 0.00% | 21.11% | 78.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0334134018 | G -> A | LOC_Os03g60010.1 | synonymous_variant ; p.Gln529Gln; LOW | synonymous_codon | Average:5.173; most accessible tissue: Minghui63 flower, score: 7.958 | N | N | N | N |
| vg0334134018 | G -> DEL | LOC_Os03g60010.1 | N | frameshift_variant | Average:5.173; most accessible tissue: Minghui63 flower, score: 7.958 | N | N | N | N |