| Variant ID: vg0318608541 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 18608541 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 122. )
AGCCCCTTCGCCTGCTGCTGCCCGCCCTGTCCTCCCAAGCCGCCATATAGAAAAAAAATTCAAAGGTGGTGCCGGTGATTGCAAAGCGAGCGCTCGGGGC[G/A]
GGGCGGGGAGGGGCGTACCTTGGAGTCCGCGACGAGGCGGACGTAGTCCCAGCTGAGGACGATCTTGTGGAAGCGGTCCATGGTGGAGGCGGCGACGCCC
GGGCGTCGCCGCCTCCACCATGGACCGCTTCCACAAGATCGTCCTCAGCTGGGACTACGTCCGCCTCGTCGCGGACTCCAAGGTACGCCCCTCCCCGCCC[C/T]
GCCCCGAGCGCTCGCTTTGCAATCACCGGCACCACCTTTGAATTTTTTTTCTATATGGCGGCTTGGGAGGACAGGGCGGGCAGCAGCAGGCGAAGGGGCT
| 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 | 76.40% | 0.10% | 9.06% | 14.47% | NA |
| All Indica | 2759 | 71.00% | 0.10% | 9.82% | 19.03% | NA |
| All Japonica | 1512 | 88.80% | 0.00% | 2.05% | 9.19% | NA |
| Aus | 269 | 52.40% | 0.00% | 44.24% | 3.35% | NA |
| Indica I | 595 | 77.00% | 0.00% | 8.57% | 14.45% | NA |
| Indica II | 465 | 82.20% | 0.20% | 6.67% | 10.97% | NA |
| Indica III | 913 | 66.40% | 0.00% | 8.43% | 25.19% | NA |
| Indica Intermediate | 786 | 65.40% | 0.30% | 14.25% | 20.10% | NA |
| Temperate Japonica | 767 | 99.90% | 0.00% | 0.00% | 0.13% | NA |
| Tropical Japonica | 504 | 73.00% | 0.00% | 3.77% | 23.21% | NA |
| Japonica Intermediate | 241 | 86.30% | 0.00% | 4.98% | 8.71% | NA |
| VI/Aromatic | 96 | 94.80% | 2.10% | 3.12% | 0.00% | NA |
| Intermediate | 90 | 83.30% | 0.00% | 4.44% | 12.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0318608541 | G -> A | LOC_Os03g32540.1 | upstream_gene_variant ; 2652.0bp to feature; MODIFIER | silent_mutation | Average:31.763; most accessible tissue: Minghui63 young leaf, score: 61.007 | N | N | N | N |
| vg0318608541 | G -> A | LOC_Os03g32526.1 | intron_variant ; MODIFIER | silent_mutation | Average:31.763; most accessible tissue: Minghui63 young leaf, score: 61.007 | N | N | N | N |
| vg0318608541 | G -> DEL | N | N | silent_mutation | Average:31.763; most accessible tissue: Minghui63 young leaf, score: 61.007 | N | N | N | N |