| Variant ID: vg0420968033 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 20968033 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
GCTATGGGGAACTTGAGACATAATTTCACCAGAAAAAGTGCTTTCCATGGTTTTAGATAATATGCCAGGCTAGCAAAATGCTCCATCGATTCTATGCGAT[C/A]
TCTCTTCAAGAAAGAAGTTATGATTGAAAATTCATAACATTGATATATATCTGCACTTTTGTAGTTTGAAGAGGGAGTGACCCCCAGTGCATATGCCTTT
AAAGGCATATGCACTGGGGGTCACTCCCTCTTCAAACTACAAAAGTGCAGATATATATCAATGTTATGAATTTTCAATCATAACTTCTTTCTTGAAGAGA[G/T]
ATCGCATAGAATCGATGGAGCATTTTGCTAGCCTGGCATATTATCTAAAACCATGGAAAGCACTTTTTCTGGTGAAATTATGTCTCAAGTTCCCCATAGC
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 96.40% | 0.70% | 0.66% | 2.20% | NA |
| All Indica | 2759 | 98.50% | 1.10% | 0.33% | 0.07% | NA |
| All Japonica | 1512 | 93.20% | 0.20% | 0.66% | 5.95% | NA |
| Aus | 269 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.30% | 0.50% | 0.00% | 0.17% | NA |
| Indica II | 465 | 95.70% | 3.20% | 0.86% | 0.22% | NA |
| Indica III | 913 | 99.70% | 0.10% | 0.22% | 0.00% | NA |
| Indica Intermediate | 786 | 98.20% | 1.40% | 0.38% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 82.50% | 0.60% | 1.98% | 14.88% | NA |
| Japonica Intermediate | 241 | 93.80% | 0.00% | 0.00% | 6.22% | NA |
| VI/Aromatic | 96 | 76.00% | 1.00% | 12.50% | 10.42% | NA |
| Intermediate | 90 | 97.80% | 0.00% | 0.00% | 2.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0420968033 | C -> DEL | N | N | silent_mutation | Average:18.058; most accessible tissue: Zhenshan97 flower, score: 34.767 | N | N | N | N |
| vg0420968033 | C -> A | LOC_Os04g34650.1 | upstream_gene_variant ; 3365.0bp to feature; MODIFIER | silent_mutation | Average:18.058; most accessible tissue: Zhenshan97 flower, score: 34.767 | N | N | N | N |
| vg0420968033 | C -> A | LOC_Os04g34670.1 | intron_variant ; MODIFIER | silent_mutation | Average:18.058; most accessible tissue: Zhenshan97 flower, score: 34.767 | N | N | N | N |