| Variant ID: vg1218480937 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 18480937 |
| 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: 39. )
CAGTGCGACTAGCTGTTCGACGAGGTCGACTGCGATAGATGATTGTGAATCAAGCTTAAAATCTTGCACCTAGGCGTCCTCCTCCTTTCCTTGCCGAAGG[G/A]
ATTTTCCTCTGTTTTTTGAGATCGCAAAGACAAGCGGCATGAGGTCTTTGGGTCTTTGCCCACCAATCCATGCGGACTCCCAAAATCGCACCGTGTTTCC
GGAAACACGGTGCGATTTTGGGAGTCCGCATGGATTGGTGGGCAAAGACCCAAAGACCTCATGCCGCTTGTCTTTGCGATCTCAAAAAACAGAGGAAAAT[C/T]
CCTTCGGCAAGGAAAGGAGGAGGACGCCTAGGTGCAAGATTTTAAGCTTGATTCACAATCATCTATCGCAGTCGACCTCGTCGAACAGCTAGTCGCACTG
| 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 | 18.60% | 1.10% | 11.26% | 69.11% | NA |
| All Indica | 2759 | 5.80% | 0.70% | 10.84% | 82.71% | NA |
| All Japonica | 1512 | 40.90% | 0.00% | 4.50% | 54.63% | NA |
| Aus | 269 | 4.50% | 11.20% | 50.56% | 33.83% | NA |
| Indica I | 595 | 5.00% | 0.00% | 5.88% | 89.08% | NA |
| Indica II | 465 | 7.70% | 0.00% | 6.02% | 86.24% | NA |
| Indica III | 913 | 6.00% | 0.50% | 16.10% | 77.33% | NA |
| Indica Intermediate | 786 | 4.80% | 1.80% | 11.32% | 82.06% | NA |
| Temperate Japonica | 767 | 60.60% | 0.00% | 1.17% | 38.20% | NA |
| Tropical Japonica | 504 | 17.70% | 0.00% | 10.71% | 71.63% | NA |
| Japonica Intermediate | 241 | 26.60% | 0.00% | 2.07% | 71.37% | NA |
| VI/Aromatic | 96 | 57.30% | 0.00% | 15.62% | 27.08% | NA |
| Intermediate | 90 | 37.80% | 1.10% | 15.56% | 45.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1218480937 | G -> DEL | N | N | silent_mutation | Average:13.265; most accessible tissue: Minghui63 panicle, score: 29.741 | N | N | N | N |
| vg1218480937 | G -> A | LOC_Os12g30770.1 | upstream_gene_variant ; 1624.0bp to feature; MODIFIER | silent_mutation | Average:13.265; most accessible tissue: Minghui63 panicle, score: 29.741 | N | N | N | N |
| vg1218480937 | G -> A | LOC_Os12g30790.1 | downstream_gene_variant ; 3969.0bp to feature; MODIFIER | silent_mutation | Average:13.265; most accessible tissue: Minghui63 panicle, score: 29.741 | N | N | N | N |
| vg1218480937 | G -> A | LOC_Os12g30780.1 | intron_variant ; MODIFIER | silent_mutation | Average:13.265; most accessible tissue: Minghui63 panicle, score: 29.741 | N | N | N | N |