| Variant ID: vg1217386152 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 17386152 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 90. )
TCCTAAGAAAAAAACCGTATCGATTTTAAAGAAGATGAATGGCCTAACATCATAAACGTTATTTAAAAAGCGGAATTTCATCCTTAGTGAGTTAATTACG[C/T]
TTAATCCTATTAGTTCAGAGCCCATATATAGATTAAAAGTCTACTAAACTTTCTACAAATGCTCTCAAACAGCCACGTGGCTCTCTTACAAACACTCCAA
TTGGAGTGTTTGTAAGAGAGCCACGTGGCTGTTTGAGAGCATTTGTAGAAAGTTTAGTAGACTTTTAATCTATATATGGGCTCTGAACTAATAGGATTAA[G/A]
CGTAATTAACTCACTAAGGATGAAATTCCGCTTTTTAAATAACGTTTATGATGTTAGGCCATTCATCTTCTTTAAAATCGATACGGTTTTTTTCTTAGGA
| 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 | 61.50% | 23.70% | 4.95% | 9.86% | NA |
| All Indica | 2759 | 55.00% | 28.10% | 4.24% | 12.61% | NA |
| All Japonica | 1512 | 75.00% | 10.80% | 7.01% | 7.21% | NA |
| Aus | 269 | 66.20% | 30.90% | 1.12% | 1.86% | NA |
| Indica I | 595 | 83.40% | 6.60% | 3.70% | 6.39% | NA |
| Indica II | 465 | 69.90% | 17.00% | 4.09% | 9.03% | NA |
| Indica III | 913 | 28.10% | 51.50% | 3.07% | 17.31% | NA |
| Indica Intermediate | 786 | 56.00% | 23.90% | 6.11% | 13.99% | NA |
| Temperate Japonica | 767 | 77.80% | 0.90% | 11.99% | 9.26% | NA |
| Tropical Japonica | 504 | 67.70% | 27.60% | 0.40% | 4.37% | NA |
| Japonica Intermediate | 241 | 81.30% | 7.10% | 4.98% | 6.64% | NA |
| VI/Aromatic | 96 | 15.60% | 81.20% | 1.04% | 2.08% | NA |
| Intermediate | 90 | 66.70% | 23.30% | 7.78% | 2.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1217386152 | C -> DEL | N | N | silent_mutation | Average:31.31; most accessible tissue: Zhenshan97 panicle, score: 61.671 | N | N | N | N |
| vg1217386152 | C -> T | LOC_Os12g29320-LOC_Os12g29330 | intergenic_region ; MODIFIER | silent_mutation | Average:31.31; most accessible tissue: Zhenshan97 panicle, score: 61.671 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1217386152 | NA | 4.59E-06 | mr1014 | Ind_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 |
| vg1217386152 | 1.40E-06 | 3.47E-09 | mr1004_2 | 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 |
| vg1217386152 | 1.98E-06 | 2.53E-07 | mr1004_2 | Ind_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 |
| vg1217386152 | 1.07E-06 | 3.36E-07 | mr1011_2 | Ind_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 |
| vg1217386152 | NA | 1.99E-07 | mr1015_2 | Ind_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 |