| Variant ID: vg0605309508 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 5309508 |
| Reference Allele: G | Alternative Allele: C |
| Primary Allele: G | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
TATGTTGTAATACCCTAGAAAAATGTTGTTAGGTGAGGCATCCTGCAGCAACGTGGCCTTCATTGTATCCATCAGGAGACAGGATTTTGAAAAAGGGGGG[G/C]
GGGGGGAAGGTGATTGATTGGCTCGTTGAATTTTTGATGATTTTTATAATGTCTATTTCATAGTATTAATAGTAGTATGCACAAGAAATAAACGTGCTGA
TCAGCACGTTTATTTCTTGTGCATACTACTATTAATACTATGAAATAGACATTATAAAAATCATCAAAAATTCAACGAGCCAATCAATCACCTTCCCCCC[C/G]
CCCCCCTTTTTCAAAATCCTGTCTCCTGATGGATACAATGAAGGCCACGTTGCTGCAGGATGCCTCACCTAACAACATTTTTCTAGGGTATTACAACATA
| Populations | Population Size | Frequency of G(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 93.50% | 0.10% | 4.85% | 1.59% | NA |
| All Indica | 2759 | 89.50% | 0.10% | 7.72% | 2.61% | NA |
| All Japonica | 1512 | 99.70% | 0.00% | 0.33% | 0.00% | NA |
| Aus | 269 | 96.70% | 0.00% | 3.35% | 0.00% | NA |
| Indica I | 595 | 90.40% | 0.00% | 8.40% | 1.18% | NA |
| Indica II | 465 | 84.50% | 0.00% | 8.82% | 6.67% | NA |
| Indica III | 913 | 93.40% | 0.10% | 5.04% | 1.42% | NA |
| Indica Intermediate | 786 | 87.30% | 0.40% | 9.67% | 2.67% | NA |
| Temperate Japonica | 767 | 99.60% | 0.00% | 0.39% | 0.00% | NA |
| Tropical Japonica | 504 | 99.80% | 0.00% | 0.20% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.00% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 94.40% | 0.00% | 2.22% | 3.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0605309508 | G -> C | LOC_Os06g10320.1 | downstream_gene_variant ; 2777.0bp to feature; MODIFIER | silent_mutation | Average:73.246; most accessible tissue: Minghui63 young leaf, score: 82.907 | N | N | N | N |
| vg0605309508 | G -> C | LOC_Os06g10330.1 | downstream_gene_variant ; 1761.0bp to feature; MODIFIER | silent_mutation | Average:73.246; most accessible tissue: Minghui63 young leaf, score: 82.907 | N | N | N | N |
| vg0605309508 | G -> C | LOC_Os06g10340.1 | intron_variant ; MODIFIER | silent_mutation | Average:73.246; most accessible tissue: Minghui63 young leaf, score: 82.907 | N | N | N | N |
| vg0605309508 | G -> DEL | N | N | silent_mutation | Average:73.246; most accessible tissue: Minghui63 young leaf, score: 82.907 | N | N | N | N |