| Variant ID: vg0430653642 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 30653642 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.95, A: 0.04, others allele: 0.00, population size: 99. )
TCTTGGTTTTAAGGCCTTTGAGGATTTCTGCATTGGCGCGCTCCACTTGGCCATTGCTTCTGGGGTGGGCAGGTGAGGCGAAGCAGAGCTTGATGCCCAT[G/A]
TCTTCGCAGTAGTCGCCGAAGAGTTCACTAGTGAATTGGGTGCCATTATCCGTAATGATACGGTTAGGCACTCCAAAACGGGCCGTGATGCCCTTAATGA
TCATTAAGGGCATCACGGCCCGTTTTGGAGTGCCTAACCGTATCATTACGGATAATGGCACCCAATTCACTAGTGAACTCTTCGGCGACTACTGCGAAGA[C/T]
ATGGGCATCAAGCTCTGCTTCGCCTCACCTGCCCACCCCAGAAGCAATGGCCAAGTGGAGCGCGCCAATGCAGAAATCCTCAAAGGCCTTAAAACCAAGA
| 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 | 0.10% | 0.10% | 10.73% | 89.00% | NA |
| All Indica | 2759 | 0.10% | 0.10% | 14.50% | 85.28% | NA |
| All Japonica | 1512 | 0.00% | 0.00% | 3.44% | 96.56% | NA |
| Aus | 269 | 1.50% | 1.10% | 18.96% | 78.44% | NA |
| Indica I | 595 | 0.20% | 0.20% | 9.75% | 89.92% | NA |
| Indica II | 465 | 0.00% | 0.00% | 8.60% | 91.40% | NA |
| Indica III | 913 | 0.00% | 0.20% | 22.45% | 77.33% | NA |
| Indica Intermediate | 786 | 0.30% | 0.00% | 12.34% | 87.40% | NA |
| Temperate Japonica | 767 | 0.00% | 0.00% | 4.04% | 95.96% | NA |
| Tropical Japonica | 504 | 0.00% | 0.00% | 1.59% | 98.41% | NA |
| Japonica Intermediate | 241 | 0.00% | 0.00% | 5.39% | 94.61% | NA |
| VI/Aromatic | 96 | 0.00% | 0.00% | 0.00% | 100.00% | NA |
| Intermediate | 90 | 0.00% | 0.00% | 4.44% | 95.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0430653642 | G -> DEL | LOC_Os04g51730.1 | N | frameshift_variant | Average:11.428; most accessible tissue: Minghui63 panicle, score: 20.733 | N | N | N | N |
| vg0430653642 | G -> A | LOC_Os04g51730.1 | synonymous_variant ; p.Asp240Asp; LOW | synonymous_codon | Average:11.428; most accessible tissue: Minghui63 panicle, score: 20.733 | N | N | N | N |