| Variant ID: vg1120597012 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 20597012 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 340. )
TGCATACTGGTTTCGCATCGAACATCAGGAAGCTAGTATCAATGAAGGATTTGTCCATTTCGGGATACAATGCGCATGACTGTCATAGGTTGCTAACGGT[G/A]
TTCCTACCAATTGCTATAAGGGCAGTCAAACCAGTCCATACAAAGGTGGTTATAACAAAGTTGTGCTACTTTTTCAATCGAATTTCGCAGAAAGTATTTG
CAAATACTTTCTGCGAAATTCGATTGAAAAAGTAGCACAACTTTGTTATAACCACCTTTGTATGGACTGGTTTGACTGCCCTTATAGCAATTGGTAGGAA[C/T]
ACCGTTAGCAACCTATGACAGTCATGCGCATTGTATCCCGAAATGGACAAATCCTTCATTGATACTAGCTTCCTGATGTTCGATGCGAAACCAGTATGCA
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 10.10% | 0.00% | 23.00% | 66.89% | NA |
| All Indica | 2759 | 13.90% | 0.00% | 21.35% | 64.73% | NA |
| All Japonica | 1512 | 1.10% | 0.00% | 24.40% | 74.54% | NA |
| Aus | 269 | 24.50% | 0.00% | 22.68% | 52.79% | NA |
| Indica I | 595 | 28.70% | 0.20% | 20.00% | 51.09% | NA |
| Indica II | 465 | 6.20% | 0.00% | 21.08% | 72.69% | NA |
| Indica III | 913 | 9.60% | 0.00% | 21.58% | 68.78% | NA |
| Indica Intermediate | 786 | 12.10% | 0.00% | 22.26% | 65.65% | NA |
| Temperate Japonica | 767 | 0.30% | 0.00% | 27.38% | 72.36% | NA |
| Tropical Japonica | 504 | 2.20% | 0.00% | 22.02% | 75.79% | NA |
| Japonica Intermediate | 241 | 1.20% | 0.00% | 19.92% | 78.84% | NA |
| VI/Aromatic | 96 | 6.20% | 1.00% | 35.42% | 57.29% | NA |
| Intermediate | 90 | 5.60% | 0.00% | 37.78% | 56.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1120597012 | G -> A | LOC_Os11g35130.1 | synonymous_variant ; p.Val561Val; LOW | synonymous_codon | Average:4.371; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg1120597012 | G -> DEL | LOC_Os11g35130.1 | N | frameshift_variant | Average:4.371; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |