| Variant ID: vg1200521827 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 521827 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.96, T: 0.03, others allele: 0.00, population size: 107. )
CGAACACGCAGAACGTGCACGACAGCGACAGCGCGCGCCACCGTCGGGTCGTCGCCGACGTCGAACAGCCCGCCGGCCCACTCCGGCTTCGCGACCACCG[C/T]
CCTGTTTCTGTTGCTGTCACACTGCGCCGTCACCGCGATCGCGTTGGCCTCGTCGACCTGCGATTTCACGTTCTCGTCGTCGGTGGACGCCGGGATCAGC
GCTGATCCCGGCGTCCACCGACGACGAGAACGTGAAATCGCAGGTCGACGAGGCCAACGCGATCGCGGTGACGGCGCAGTGTGACAGCAACAGAAACAGG[G/A]
CGGTGGTCGCGAAGCCGGAGTGGGCCGGCGGGCTGTTCGACGTCGGCGACGACCCGACGGTGGCGCGCGCTGTCGCTGTCGTGCACGTTCTGCGTGTTCG
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 71.50% | 27.70% | 0.83% | 0.00% | NA |
| All Indica | 2759 | 54.00% | 44.70% | 1.30% | 0.00% | NA |
| All Japonica | 1512 | 96.80% | 3.20% | 0.00% | 0.00% | NA |
| Aus | 269 | 97.40% | 1.50% | 1.12% | 0.00% | NA |
| Indica I | 595 | 90.10% | 9.20% | 0.67% | 0.00% | NA |
| Indica II | 465 | 22.20% | 77.00% | 0.86% | 0.00% | NA |
| Indica III | 913 | 46.80% | 52.20% | 0.99% | 0.00% | NA |
| Indica Intermediate | 786 | 53.80% | 43.80% | 2.42% | 0.00% | NA |
| Temperate Japonica | 767 | 95.40% | 4.60% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 98.00% | 2.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 98.80% | 1.20% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 77.80% | 22.20% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1200521827 | C -> T | LOC_Os12g01890.1 | missense_variant ; p.Ala286Thr; MODERATE | nonsynonymous_codon ; A286T | Average:66.856; most accessible tissue: Zhenshan97 flower, score: 86.118 | unknown | unknown | TOLERATED | 0.33 |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1200521827 | NA | 3.13E-15 | Grain_length | 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 |
| vg1200521827 | NA | 2.61E-16 | Grain_length | Ind_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 |
| vg1200521827 | NA | 3.01E-08 | mr1174 | All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
| vg1200521827 | NA | 3.78E-09 | mr1174_2 | All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |