| Variant ID: vg0143000749 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 43000749 |
| 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: 250. )
CATTCTTTAACCCGAAGGGCATTGTCGTATAACAATAGGTTCCTATGGGGGTAATGAACGCAGTTTTTTCCTCATCCTCCCTAGCCATGCGAATCTGATG[G/A]
TAACCAGAGTATGCATCTAGAAAACACAAAAGGTCACACCCCGCAGTGGAGTCGACAATCTGATCTATGCGAGGCAGGGGGTAAGGATCCTTAGGACATG
CATGTCCTAAGGATCCTTACCCCCTGCCTCGCATAGATCAGATTGTCGACTCCACTGCGGGGTGTGACCTTTTGTGTTTTCTAGATGCATACTCTGGTTA[C/T]
CATCAGATTCGCATGGCTAGGGAGGATGAGGAAAAAACTGCGTTCATTACCCCCATAGGAACCTATTGTTATACGACAATGCCCTTCGGGTTAAAGAATG
| 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 | 38.90% | 0.10% | 19.11% | 41.87% | NA |
| All Indica | 2759 | 49.60% | 0.20% | 23.49% | 26.75% | NA |
| All Japonica | 1512 | 22.40% | 0.00% | 6.22% | 71.43% | NA |
| Aus | 269 | 26.00% | 0.40% | 43.12% | 30.48% | NA |
| Indica I | 595 | 26.90% | 0.00% | 26.55% | 46.55% | NA |
| Indica II | 465 | 33.50% | 0.00% | 33.76% | 32.69% | NA |
| Indica III | 913 | 75.90% | 0.30% | 14.57% | 9.20% | NA |
| Indica Intermediate | 786 | 45.70% | 0.30% | 25.45% | 28.63% | NA |
| Temperate Japonica | 767 | 39.10% | 0.00% | 1.83% | 59.06% | NA |
| Tropical Japonica | 504 | 5.00% | 0.00% | 11.90% | 83.13% | NA |
| Japonica Intermediate | 241 | 5.40% | 0.00% | 8.30% | 86.31% | NA |
| VI/Aromatic | 96 | 28.10% | 0.00% | 21.88% | 50.00% | NA |
| Intermediate | 90 | 38.90% | 0.00% | 26.67% | 34.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0143000749 | G -> A | LOC_Os01g74230.1 | synonymous_variant ; p.Tyr751Tyr; LOW | synonymous_codon | Average:14.858; most accessible tissue: Zhenshan97 panicle, score: 28.447 | N | N | N | N |
| vg0143000749 | G -> DEL | LOC_Os01g74230.1 | N | frameshift_variant | Average:14.858; most accessible tissue: Zhenshan97 panicle, score: 28.447 | N | N | N | N |