| Variant ID: vg0409515288 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 9515288 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 281. )
CTTTAGACACAACATTATAGATTTGAAACGGTCCTTCCCAATTTGGTGACCACTTGCCGAACTTGTTATCCCGAGTTCCAATCGGCAAAATCAACTTCCA[T/A]
ACAAGTTCACCTTCCGAAAAATCCTTAGGCACTACTTTCTTGTTATAATGCCTAGCAACTCGTTCCTTATCTCTGGTAACCTTAGCAAGGGCTCGTAAAC
GTTTACGAGCCCTTGCTAAGGTTACCAGAGATAAGGAACGAGTTGCTAGGCATTATAACAAGAAAGTAGTGCCTAAGGATTTTTCGGAAGGTGAACTTGT[A/T]
TGGAAGTTGATTTTGCCGATTGGAACTCGGGATAACAAGTTCGGCAAGTGGTCACCAAATTGGGAAGGACCGTTTCAAATCTATAATGTTGTGTCTAAAG
| Populations | Population Size | Frequency of T(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 91.00% | 0.30% | 0.32% | 8.38% | NA |
| All Indica | 2759 | 99.70% | 0.30% | 0.07% | 0.00% | NA |
| All Japonica | 1512 | 74.50% | 0.00% | 0.60% | 24.87% | NA |
| Aus | 269 | 98.10% | 1.50% | 0.37% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 99.60% | 0.20% | 0.22% | 0.00% | NA |
| Indica III | 913 | 99.20% | 0.70% | 0.11% | 0.00% | NA |
| Indica Intermediate | 786 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 98.60% | 0.00% | 0.00% | 1.43% | NA |
| Tropical Japonica | 504 | 34.50% | 0.00% | 1.39% | 64.09% | NA |
| Japonica Intermediate | 241 | 81.70% | 0.00% | 0.83% | 17.43% | NA |
| VI/Aromatic | 96 | 74.00% | 4.20% | 2.08% | 19.79% | NA |
| Intermediate | 90 | 97.80% | 0.00% | 1.11% | 1.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0409515288 | T -> DEL | LOC_Os04g17380.1 | N | frameshift_variant | Average:29.115; most accessible tissue: Minghui63 young leaf, score: 42.042 | N | N | N | N |
| vg0409515288 | T -> A | LOC_Os04g17380.1 | synonymous_variant ; p.Val106Val; LOW | synonymous_codon | Average:29.115; most accessible tissue: Minghui63 young leaf, score: 42.042 | N | N | N | N |