| Variant ID: vg0101920420 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 1920420 |
| 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: 295. )
TCCTAGCCATAGACAAGAGTACCGACCCAATCCCACCTACGGCCGGAACCCCCGGGACAGGCAGGCAGGACTGAGCCCCTAGCAGCAGGACACCGGCCCT[G/A]
TGCCATGACATCTCGACTACCGGGCCGCAGCTCGTGTAGCCTTCATTTGCCCTGGAGAATGTCCATCGACCCCCGACTTCATCCATCTCCATCCGTGTAC
GTACACGGATGGAGATGGATGAAGTCGGGGGTCGATGGACATTCTCCAGGGCAAATGAAGGCTACACGAGCTGCGGCCCGGTAGTCGAGATGTCATGGCA[C/T]
AGGGCCGGTGTCCTGCTGCTAGGGGCTCAGTCCTGCCTGCCTGTCCCGGGGGTTCCGGCCGTAGGTGGGATTGGGTCGGTACTCTTGTCTATGGCTAGGA
| 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 | 89.20% | 0.10% | 1.80% | 8.87% | NA |
| All Indica | 2759 | 92.00% | 0.20% | 2.75% | 5.04% | NA |
| All Japonica | 1512 | 81.50% | 0.00% | 0.46% | 18.06% | NA |
| Aus | 269 | 99.60% | 0.00% | 0.00% | 0.37% | NA |
| Indica I | 595 | 83.20% | 0.00% | 4.03% | 12.77% | NA |
| Indica II | 465 | 91.20% | 0.40% | 4.73% | 3.66% | NA |
| Indica III | 913 | 96.70% | 0.40% | 1.31% | 1.53% | NA |
| Indica Intermediate | 786 | 93.60% | 0.00% | 2.29% | 4.07% | NA |
| Temperate Japonica | 767 | 88.90% | 0.00% | 0.26% | 10.82% | NA |
| Tropical Japonica | 504 | 78.40% | 0.00% | 0.79% | 20.83% | NA |
| Japonica Intermediate | 241 | 64.30% | 0.00% | 0.41% | 35.27% | NA |
| VI/Aromatic | 96 | 99.00% | 0.00% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 92.20% | 0.00% | 1.11% | 6.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0101920420 | G -> A | LOC_Os01g04310.1 | synonymous_variant ; p.His4His; LOW | synonymous_codon | Average:6.858; most accessible tissue: Zhenshan97 flag leaf, score: 10.769 | N | N | N | N |
| vg0101920420 | G -> DEL | LOC_Os01g04310.1 | N | frameshift_variant | Average:6.858; most accessible tissue: Zhenshan97 flag leaf, score: 10.769 | N | N | N | N |