| Variant ID: vg1213685109 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 13685109 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 218. )
CTCTCCTGCCGAGTGGAAAAGTTCCCAATCACTTATCTTGGACTCCCTCTCTCCACTAGGAAACCAACGAAGGCCGAGATCCAGCCGATCCTTGATAGGC[T/A]
GGCAAAGAAGGTAGCCGGTTGGAAGCCGAAAATGCTGTCTATTGATGGGCGACTGTGCTTGATCAAGTCGGTCCTAATGGCGCTGCCGGTGCACTACATG
CATGTAGTGCACCGGCAGCGCCATTAGGACCGACTTGATCAAGCACAGTCGCCCATCAATAGACAGCATTTTCGGCTTCCAACCGGCTACCTTCTTTGCC[A/T]
GCCTATCAAGGATCGGCTGGATCTCGGCCTTCGTTGGTTTCCTAGTGGAGAGAGGGAGTCCAAGATAAGTGATTGGGAACTTTTCCACTCGGCAGGAGAG
| Populations | Population Size | Frequency of T(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 71.60% | 2.60% | 2.09% | 23.64% | NA |
| All Indica | 2759 | 73.20% | 0.20% | 2.36% | 24.28% | NA |
| All Japonica | 1512 | 63.00% | 7.50% | 2.12% | 27.31% | NA |
| Aus | 269 | 91.10% | 2.20% | 0.37% | 6.32% | NA |
| Indica I | 595 | 95.60% | 0.00% | 1.51% | 2.86% | NA |
| Indica II | 465 | 57.60% | 0.40% | 4.73% | 37.20% | NA |
| Indica III | 913 | 64.30% | 0.00% | 2.30% | 33.41% | NA |
| Indica Intermediate | 786 | 75.70% | 0.40% | 1.65% | 22.26% | NA |
| Temperate Japonica | 767 | 73.70% | 5.20% | 1.43% | 19.69% | NA |
| Tropical Japonica | 504 | 43.30% | 9.30% | 3.97% | 43.45% | NA |
| Japonica Intermediate | 241 | 70.50% | 11.20% | 0.41% | 17.84% | NA |
| VI/Aromatic | 96 | 94.80% | 0.00% | 0.00% | 5.21% | NA |
| Intermediate | 90 | 85.60% | 0.00% | 1.11% | 13.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1213685109 | T -> DEL | N | N | silent_mutation | Average:34.652; most accessible tissue: Zhenshan97 flower, score: 64.273 | N | N | N | N |
| vg1213685109 | T -> A | LOC_Os12g24070-LOC_Os12g24080 | intergenic_region ; MODIFIER | silent_mutation | Average:34.652; most accessible tissue: Zhenshan97 flower, score: 64.273 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1213685109 | 4.56E-07 | 1.81E-07 | mr1719 | Jap_All | YES | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
| vg1213685109 | 8.91E-07 | 8.91E-07 | mr1929 | Jap_All | YES | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |