| Variant ID: vg0424682893 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 24682893 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, others allele: 0.00, population size: 245. )
GAACTAGAGCCAAGTGCTCCTCGATGTAAGGAGCTACCAATGAAGAGTGTTGCAGAACAGTGAAATGGGCTTTACGGAATAAATTGTTGTCTACCGTCGT[T/A]
ATTGCTTTCCTTCCGAGAGTTCCCTTTCCCCGTAGTCTCCCTTCATGGCGTGATTCAGGTACCCCGATTGGGCGAAGGTCTTCGATAAATTCTACGCAAA
TTTGCGTAGAATTTATCGAAGACCTTCGCCCAATCGGGGTACCTGAATCACGCCATGAAGGGAGACTACGGGGAAAGGGAACTCTCGGAAGGAAAGCAAT[A/T]
ACGACGGTAGACAACAATTTATTCCGTAAAGCCCATTTCACTGTTCTGCAACACTCTTCATTGGTAGCTCCTTACATCGAGGAGCACTTGGCTCTAGTTC
| 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 | 29.70% | 0.30% | 22.98% | 47.06% | NA |
| All Indica | 2759 | 12.00% | 0.50% | 20.59% | 66.87% | NA |
| All Japonica | 1512 | 57.10% | 0.00% | 26.06% | 16.80% | NA |
| Aus | 269 | 37.20% | 0.00% | 30.11% | 32.71% | NA |
| Indica I | 595 | 10.80% | 0.20% | 25.55% | 63.53% | NA |
| Indica II | 465 | 17.60% | 0.60% | 23.23% | 58.49% | NA |
| Indica III | 913 | 8.30% | 0.40% | 16.65% | 74.59% | NA |
| Indica Intermediate | 786 | 14.00% | 0.80% | 19.85% | 65.39% | NA |
| Temperate Japonica | 767 | 85.40% | 0.00% | 9.26% | 5.35% | NA |
| Tropical Japonica | 504 | 24.00% | 0.00% | 44.25% | 31.75% | NA |
| Japonica Intermediate | 241 | 36.50% | 0.00% | 41.49% | 21.99% | NA |
| VI/Aromatic | 96 | 70.80% | 0.00% | 22.92% | 6.25% | NA |
| Intermediate | 90 | 42.20% | 0.00% | 23.33% | 34.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0424682893 | T -> DEL | N | N | silent_mutation | Average:6.182; most accessible tissue: Zhenshan97 panicle, score: 20.424 | N | N | N | N |
| vg0424682893 | T -> A | LOC_Os04g41620.1 | downstream_gene_variant ; 4814.0bp to feature; MODIFIER | silent_mutation | Average:6.182; most accessible tissue: Zhenshan97 panicle, score: 20.424 | N | N | N | N |
| vg0424682893 | T -> A | LOC_Os04g41599.1 | intron_variant ; MODIFIER | silent_mutation | Average:6.182; most accessible tissue: Zhenshan97 panicle, score: 20.424 | N | N | N | N |