| Variant ID: vg0904847664 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 4847664 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 281. )
GCACTGGAGTTAGGCTGAAACTGGAATCTTGGCGAGGATTTGTGTTTCCTTGATGCTTCCCTCCGTTGGAACTGGCGGGTTGGTTGGCCATCTTCTTCGT[C/T]
AGCAGAAAACTGAATCGACAATCTTTTGGTACATGATCAGTTCCTTCACAAAAGAAACAAGTGATCCTGCTCGTTGGACACCTATCGGGTGGATGGTCTT
AAGACCATCCACCCGATAGGTGTCCAACGAGCAGGATCACTTGTTTCTTTTGTGAAGGAACTGATCATGTACCAAAAGATTGTCGATTCAGTTTTCTGCT[G/A]
ACGAAGAAGATGGCCAACCAACCCGCCAGTTCCAACGGAGGGAAGCATCAAGGAAACACAAATCCTCGCCAAGATTCCAGTTTCAGCCTAACTCCAGTGC
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 20.20% | 0.70% | 4.49% | 74.63% | NA |
| All Indica | 2759 | 7.70% | 0.00% | 2.72% | 89.60% | NA |
| All Japonica | 1512 | 38.30% | 2.00% | 7.74% | 51.98% | NA |
| Aus | 269 | 22.70% | 0.00% | 2.60% | 74.72% | NA |
| Indica I | 595 | 7.60% | 0.00% | 1.68% | 90.76% | NA |
| Indica II | 465 | 8.20% | 0.00% | 1.94% | 89.89% | NA |
| Indica III | 913 | 4.90% | 0.00% | 3.61% | 91.46% | NA |
| Indica Intermediate | 786 | 10.70% | 0.00% | 2.93% | 86.39% | NA |
| Temperate Japonica | 767 | 46.20% | 0.00% | 3.91% | 49.93% | NA |
| Tropical Japonica | 504 | 26.20% | 1.60% | 7.94% | 64.29% | NA |
| Japonica Intermediate | 241 | 38.60% | 9.10% | 19.50% | 32.78% | NA |
| VI/Aromatic | 96 | 80.20% | 0.00% | 7.29% | 12.50% | NA |
| Intermediate | 90 | 27.80% | 3.30% | 6.67% | 62.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0904847664 | C -> DEL | LOC_Os09g09070.1 | N | frameshift_variant | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0904847664 | C -> T | LOC_Os09g09070.1 | synonymous_variant ; p.Leu258Leu; LOW | synonymous_codon | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |