| Variant ID: vg1227343078 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr12 | Position: 27343078 |
| Reference Allele: G | Alternative Allele: GCA |
| Primary Allele: GCA | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 331. )
ATCAGGGTATTTTGCTAAGAACCTACAAGATTGTGAGGTGAATGAGCTCGCCAATCTCTGAAGGGATGCCTCCTTGTAGGTAGTTGGCTCTCAAGTAACT[G/GCA]
CACACACACAGAGTAAATTAAACCTCCGCATTTCAGCTCTACAAAGTCATTAGCAGACAGATGGAGATGGAACCAAACAAGTACTAGATCGTAGCAGCAT
ATGCTGCTACGATCTAGTACTTGTTTGGTTCCATCTCCATCTGTCTGCTAATGACTTTGTAGAGCTGAAATGCGGAGGTTTAATTTACTCTGTGTGTGTG[C/TGC]
AGTTACTTGAGAGCCAACTACCTACAAGGAGGCATCCCTTCAGAGATTGGCGAGCTCATTCACCTCACAATCTTGTAGGTTCTTAGCAAAATACCCTGAT
| Populations | Population Size | Frequency of GCA(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 66.10% | 33.90% | 0.06% | 0.00% | NA |
| All Indica | 2759 | 97.00% | 2.90% | 0.11% | 0.00% | NA |
| All Japonica | 1512 | 7.20% | 92.80% | 0.00% | 0.00% | NA |
| Aus | 269 | 98.50% | 1.50% | 0.00% | 0.00% | NA |
| Indica I | 595 | 98.00% | 1.80% | 0.17% | 0.00% | NA |
| Indica II | 465 | 98.10% | 1.90% | 0.00% | 0.00% | NA |
| Indica III | 913 | 96.40% | 3.60% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 96.30% | 3.40% | 0.25% | 0.00% | NA |
| Temperate Japonica | 767 | 12.00% | 88.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 0.80% | 99.20% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 5.40% | 94.60% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 21.90% | 78.10% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 56.70% | 43.30% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1227343078 | G -> GCA | LOC_Os12g44090.1 | splice_region_variant&intron_variant ; LOW | silent_mutation | Average:60.43; most accessible tissue: Zhenshan97 panicle, score: 83.904 | N | N | N | N |
| vg1227343078 | G -> GCA | LOC_Os12g44100.1 | downstream_gene_variant ; 3043.0bp to feature; MODIFIER | silent_mutation | Average:60.43; most accessible tissue: Zhenshan97 panicle, score: 83.904 | N | N | N | N |