| Variant ID: vg0430653774 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 30653774 |
| 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: 409. )
TGAATTGGGTGCCATTATCCGTAATGATACGGTTAGGCACTCCAAAACGGGCCGTGATGCCCTTAATGAATTTAAGTGCAGAGTGCTTATCGATCTTGAC[G/A]
ACCGGATAAGCCTCGGGCCACTTAGTGAACTTGTCGATCGCGACATACAGATACTCAAACCCGCCCGGGGCCCGCTTAAACGGTCCCAGGATATCGAGCC
GGCTCGATATCCTGGGACCGTTTAAGCGGGCCCCGGGCGGGTTTGAGTATCTGTATGTCGCGATCGACAAGTTCACTAAGTGGCCCGAGGCTTATCCGGT[C/T]
GTCAAGATCGATAAGCACTCTGCACTTAAATTCATTAAGGGCATCACGGCCCGTTTTGGAGTGCCTAACCGTATCATTACGGATAATGGCACCCAATTCA
| 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 | 47.00% | 0.10% | 14.98% | 37.96% | NA |
| All Indica | 2759 | 49.90% | 0.10% | 14.28% | 35.74% | NA |
| All Japonica | 1512 | 41.80% | 0.10% | 11.51% | 46.56% | NA |
| Aus | 269 | 49.10% | 0.00% | 33.46% | 17.47% | NA |
| Indica I | 595 | 25.90% | 0.00% | 12.10% | 62.02% | NA |
| Indica II | 465 | 43.70% | 0.20% | 19.78% | 36.34% | NA |
| Indica III | 913 | 72.70% | 0.20% | 12.81% | 14.24% | NA |
| Indica Intermediate | 786 | 45.20% | 0.00% | 14.38% | 40.46% | NA |
| Temperate Japonica | 767 | 63.20% | 0.00% | 0.78% | 35.98% | NA |
| Tropical Japonica | 504 | 15.50% | 0.40% | 26.19% | 57.94% | NA |
| Japonica Intermediate | 241 | 28.60% | 0.00% | 14.94% | 56.43% | NA |
| VI/Aromatic | 96 | 34.40% | 0.00% | 34.38% | 31.25% | NA |
| Intermediate | 90 | 51.10% | 0.00% | 18.89% | 30.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0430653774 | G -> DEL | LOC_Os04g51730.1 | N | frameshift_variant | Average:11.246; most accessible tissue: Minghui63 panicle, score: 20.733 | N | N | N | N |
| vg0430653774 | G -> A | LOC_Os04g51730.1 | synonymous_variant ; p.Val196Val; LOW | synonymous_codon | Average:11.246; most accessible tissue: Minghui63 panicle, score: 20.733 | N | N | N | N |