| Variant ID: vg1217858893 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 17858893 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
GCCGCCACATCTCTGGGGTGAGAGCCGCCGCCGCCTCCCTCTCTCTCTCGATGAACTTAACGTACATTAACGTGAACGAACGAACGTTGGTGAACGAAAC[G/A]
TGAACTTAACGAGAACGCAAACGTGAACGATCGTGAACGAAACGTGAACGTAACGAGAACGCGAACGTGAACGAACGTGAATGAAACGCGAACGGACGTG
CACGTCCGTTCGCGTTTCATTCACGTTCGTTCACGTTCGCGTTCTCGTTACGTTCACGTTTCGTTCACGATCGTTCACGTTTGCGTTCTCGTTAAGTTCA[C/T]
GTTTCGTTCACCAACGTTCGTTCGTTCACGTTAATGTACGTTAAGTTCATCGAGAGAGAGAGGGAGGCGGCGGCGGCTCTCACCCCAGAGATGTGGCGGC
| 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 | 72.90% | 2.10% | 1.33% | 23.70% | NA |
| All Indica | 2759 | 71.80% | 1.20% | 0.69% | 26.31% | NA |
| All Japonica | 1512 | 75.80% | 0.10% | 2.78% | 21.30% | NA |
| Aus | 269 | 70.60% | 23.80% | 0.74% | 4.83% | NA |
| Indica I | 595 | 92.10% | 0.20% | 0.17% | 7.56% | NA |
| Indica II | 465 | 68.00% | 3.00% | 0.43% | 28.60% | NA |
| Indica III | 913 | 59.90% | 0.90% | 0.99% | 38.23% | NA |
| Indica Intermediate | 786 | 72.60% | 1.10% | 0.89% | 25.32% | NA |
| Temperate Japonica | 767 | 94.40% | 0.30% | 3.52% | 1.83% | NA |
| Tropical Japonica | 504 | 51.60% | 0.00% | 2.18% | 46.23% | NA |
| Japonica Intermediate | 241 | 67.20% | 0.00% | 1.66% | 31.12% | NA |
| VI/Aromatic | 96 | 50.00% | 0.00% | 0.00% | 50.00% | NA |
| Intermediate | 90 | 87.80% | 0.00% | 0.00% | 12.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1217858893 | G -> DEL | N | N | silent_mutation | Average:25.232; most accessible tissue: Zhenshan97 flag leaf, score: 51.466 | N | N | N | N |
| vg1217858893 | G -> A | LOC_Os12g29860.1 | intron_variant ; MODIFIER | silent_mutation | Average:25.232; most accessible tissue: Zhenshan97 flag leaf, score: 51.466 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1217858893 | 1.04E-11 | 4.63E-22 | Awn_length | All | YES | Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652 |
| vg1217858893 | 3.95E-08 | 3.89E-16 | Awn_length | Jap_All | Not | Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652 |