| Variant ID: vg0121065777 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 21065777 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 300. )
CATGAATGTTCCCCAACTGATGATGATTTTGAGAGATGTCAGATTCCCACTGATTCTGACATTGAAAGACTTAGAGAGGAAGAAGATAATGAAGAGGACA[A/G]
TTTCCAAGAGGTGTCTAACAAAAAGAAGAACAGGGCTAAGAAAACAGAACTTGCAGTGACTTCAAGGATGAATCTAAGACAAAGGGAGATGGCTGCTAAC
GTTAGCAGCCATCTCCCTTTGTCTTAGATTCATCCTTGAAGTCACTGCAAGTTCTGTTTTCTTAGCCCTGTTCTTCTTTTTGTTAGACACCTCTTGGAAA[T/C]
TGTCCTCTTCATTATCTTCTTCCTCTCTAAGTCTTTCAATGTCAGAATCAGTGGGAATCTGACATCTCTCAAAATCATCATCAGTTGGGGAACATTCATG
| 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 | 97.60% | 0.20% | 0.15% | 2.03% | NA |
| All Indica | 2759 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 93.30% | 0.00% | 0.46% | 6.22% | NA |
| Aus | 269 | 98.10% | 1.90% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 99.60% | 0.00% | 0.00% | 0.39% | NA |
| Tropical Japonica | 504 | 95.60% | 0.00% | 0.00% | 4.37% | NA |
| Japonica Intermediate | 241 | 68.50% | 0.00% | 2.90% | 28.63% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 97.80% | 0.00% | 0.00% | 2.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0121065777 | A -> G | LOC_Os01g37660.1 | missense_variant ; p.Asn106Ser; MODERATE | nonsynonymous_codon | Average:42.285; most accessible tissue: Zhenshan97 flag leaf, score: 67.785 | unknown | unknown | TOLERATED | 1.00 |
| vg0121065777 | A -> DEL | LOC_Os01g37660.1 | N | frameshift_variant | Average:42.285; most accessible tissue: Zhenshan97 flag leaf, score: 67.785 | N | N | N | N |