| Variant ID: vg0335314920 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 35314920 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.89, A: 0.10, others allele: 0.00, population size: 277. )
CACATCCCAAATGACATTACCTGGTGAGAAGTTTGACGTAGCAAGTTTCAGCTCTTCATAGGTAAACAGCCTACACGTTGAAGAGTACTTCTCTTGAAGC[G/A]
ATTCCACTTCATTTGGAGGCCATGATATATCATATAAAGAGAACGAAAACATAGATTCTGTGTCAACAGCTGAAGTGGATTCACATTCGGAATCACAATT
AATTGTGATTCCGAATGTGAATCCACTTCAGCTGTTGACACAGAATCTATGTTTTCGTTCTCTTTATATGATATATCATGGCCTCCAAATGAAGTGGAAT[C/T]
GCTTCAAGAGAAGTACTCTTCAACGTGTAGGCTGTTTACCTATGAAGAGCTGAAACTTGCTACGTCAAACTTCTCACCAGGTAATGTCATTTGGGATGTG
| 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 | 76.40% | 23.40% | 0.06% | 0.08% | NA |
| All Indica | 2759 | 60.60% | 39.20% | 0.04% | 0.14% | NA |
| All Japonica | 1512 | 99.60% | 0.30% | 0.07% | 0.00% | NA |
| Aus | 269 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Indica I | 595 | 73.60% | 26.10% | 0.00% | 0.34% | NA |
| Indica II | 465 | 43.20% | 56.10% | 0.22% | 0.43% | NA |
| Indica III | 913 | 64.50% | 35.50% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 56.60% | 43.40% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 99.60% | 0.30% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 77.80% | 21.10% | 1.11% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0335314920 | G -> A | LOC_Os03g62340.1 | missense_variant ; p.Ser569Leu; MODERATE | nonsynonymous_codon ; S569L | Average:55.547; most accessible tissue: Zhenshan97 panicle, score: 73.605 | unknown | unknown | DELETERIOUS | 0.00 |
| vg0335314920 | G -> DEL | LOC_Os03g62340.1 | N | frameshift_variant | Average:55.547; most accessible tissue: Zhenshan97 panicle, score: 73.605 | N | N | N | N |