| Variant ID: vg0605309504 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 5309504 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
GGACTATGTTGTAATACCCTAGAAAAATGTTGTTAGGTGAGGCATCCTGCAGCAACGTGGCCTTCATTGTATCCATCAGGAGACAGGATTTTGAAAAAGG[G/A]
GGGGGGGGGGAAGGTGATTGATTGGCTCGTTGAATTTTTGATGATTTTTATAATGTCTATTTCATAGTATTAATAGTAGTATGCACAAGAAATAAACGTG
CACGTTTATTTCTTGTGCATACTACTATTAATACTATGAAATAGACATTATAAAAATCATCAAAAATTCAACGAGCCAATCAATCACCTTCCCCCCCCCC[C/T]
CCTTTTTCAAAATCCTGTCTCCTGATGGATACAATGAAGGCCACGTTGCTGCAGGATGCCTCACCTAACAACATTTTTCTAGGGTATTACAACATAGTCC
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 48.50% | 0.10% | 40.71% | 10.71% | NA |
| All Indica | 2759 | 31.40% | 0.00% | 53.68% | 14.93% | NA |
| All Japonica | 1512 | 74.70% | 0.10% | 20.30% | 4.96% | NA |
| Aus | 269 | 84.00% | 0.70% | 14.13% | 1.12% | NA |
| Indica I | 595 | 29.90% | 0.00% | 59.83% | 10.25% | NA |
| Indica II | 465 | 23.70% | 0.00% | 47.53% | 28.82% | NA |
| Indica III | 913 | 35.50% | 0.00% | 54.98% | 9.53% | NA |
| Indica Intermediate | 786 | 32.20% | 0.10% | 51.15% | 16.54% | NA |
| Temperate Japonica | 767 | 75.10% | 0.00% | 19.04% | 5.87% | NA |
| Tropical Japonica | 504 | 68.80% | 0.20% | 26.98% | 3.97% | NA |
| Japonica Intermediate | 241 | 85.50% | 0.00% | 10.37% | 4.15% | NA |
| VI/Aromatic | 96 | 33.30% | 0.00% | 61.46% | 5.21% | NA |
| Intermediate | 90 | 43.30% | 1.10% | 43.33% | 12.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0605309504 | G -> A | LOC_Os06g10320.1 | downstream_gene_variant ; 2773.0bp to feature; MODIFIER | silent_mutation | Average:75.067; most accessible tissue: Minghui63 young leaf, score: 85.028 | N | N | N | N |
| vg0605309504 | G -> A | LOC_Os06g10330.1 | downstream_gene_variant ; 1757.0bp to feature; MODIFIER | silent_mutation | Average:75.067; most accessible tissue: Minghui63 young leaf, score: 85.028 | N | N | N | N |
| vg0605309504 | G -> A | LOC_Os06g10340.1 | intron_variant ; MODIFIER | silent_mutation | Average:75.067; most accessible tissue: Minghui63 young leaf, score: 85.028 | N | N | N | N |
| vg0605309504 | G -> DEL | N | N | silent_mutation | Average:75.067; most accessible tissue: Minghui63 young leaf, score: 85.028 | N | N | N | N |