| Variant ID: vg1117778392 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 17778392 |
| 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: 395. )
AGATACGAGAGGCTGCGCGACGACTAACAGATGCAGTGGAAGCCTCCTCTCAGGGCACGTTCCGACCAGACAGAGATAGGGACGAGCTGACACTCGCCCT[G/A]
CAGACTCCAGAGCATCCAGGACGAACACGAGGGAAAGGGGTGATTCCTTGGAAGATTGGTTTCAAGGAGGACATCCACACGTACAGGAGTCGGATGAGGA
TCCTCATCCGACTCCTGTACGTGTGGATGTCCTCCTTGAAACCAATCTTCCAAGGAATCACCCCTTTCCCTCGTGTTCGTCCTGGATGCTCTGGAGTCTG[C/T]
AGGGCGAGTGTCAGCTCGTCCCTATCTCTGTCTGGTCGGAACGTGCCCTGAGAGGAGGCTTCCACTGCATCTGTTAGTCGTCGCGCAGCCTCTCGTATCT
| 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 | 14.60% | 0.40% | 13.33% | 71.67% | NA |
| All Indica | 2759 | 9.90% | 0.40% | 5.80% | 83.91% | NA |
| All Japonica | 1512 | 23.90% | 0.30% | 26.32% | 49.47% | NA |
| Aus | 269 | 7.80% | 0.00% | 11.15% | 81.04% | NA |
| Indica I | 595 | 7.60% | 0.20% | 6.39% | 85.88% | NA |
| Indica II | 465 | 22.20% | 0.00% | 6.02% | 71.83% | NA |
| Indica III | 913 | 5.80% | 1.20% | 5.70% | 87.29% | NA |
| Indica Intermediate | 786 | 9.00% | 0.00% | 5.34% | 85.62% | NA |
| Temperate Japonica | 767 | 17.20% | 0.00% | 39.24% | 43.55% | NA |
| Tropical Japonica | 504 | 17.50% | 0.80% | 10.12% | 71.63% | NA |
| Japonica Intermediate | 241 | 58.90% | 0.00% | 19.09% | 21.99% | NA |
| VI/Aromatic | 96 | 20.80% | 0.00% | 29.17% | 50.00% | NA |
| Intermediate | 90 | 18.90% | 1.10% | 15.56% | 64.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1117778392 | G -> A | LOC_Os11g30552.1 | synonymous_variant ; p.Leu448Leu; LOW | synonymous_codon | Average:8.604; most accessible tissue: Zhenshan97 panicle, score: 16.188 | N | N | N | N |
| vg1117778392 | G -> DEL | LOC_Os11g30552.1 | N | frameshift_variant | Average:8.604; most accessible tissue: Zhenshan97 panicle, score: 16.188 | N | N | N | N |