| Variant ID: vg1209987334 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 9987334 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.77, A: 0.23, others allele: 0.00, population size: 213. )
TTTTCCAATTTTACTTCCATGTATGTTCAGTGTTTGTAAATTTTTCAGGTCGCCAATTTTATCCGGAAGCTCAGTGATACCTTCAGAATTGATTCTCAAA[A/T]
ACTTTAATTGGCAAAAGAATCTGAGATATTTAATATGTTGGTTTCCTAAGCTATCACAATCCTCAAATATCAATACTCTCAGATAACGGAACTTTGGGAG
CTCCCAAAGTTCCGTTATCTGAGAGTATTGATATTTGAGGATTGTGATAGCTTAGGAAACCAACATATTAAATATCTCAGATTCTTTTGCCAATTAAAGT[T/A]
TTTGAGAATCAATTCTGAAGGTATCACTGAGCTTCCGGATAAAATTGGCGACCTGAAAAATTTACAAACACTGAACATACATGGAAGTAAAATTGGAAAA
| Populations | Population Size | Frequency of A(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 60.50% | 38.20% | 0.32% | 1.02% | NA |
| All Indica | 2759 | 54.20% | 44.80% | 0.40% | 0.62% | NA |
| All Japonica | 1512 | 84.70% | 15.30% | 0.00% | 0.00% | NA |
| Aus | 269 | 2.60% | 86.60% | 0.00% | 10.78% | NA |
| Indica I | 595 | 31.10% | 68.40% | 0.50% | 0.00% | NA |
| Indica II | 465 | 76.80% | 22.20% | 0.22% | 0.86% | NA |
| Indica III | 913 | 57.00% | 42.40% | 0.44% | 0.22% | NA |
| Indica Intermediate | 786 | 55.20% | 43.00% | 0.38% | 1.40% | NA |
| Temperate Japonica | 767 | 94.30% | 5.70% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 72.00% | 28.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 80.50% | 19.50% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 22.90% | 75.00% | 1.04% | 1.04% | NA |
| Intermediate | 90 | 58.90% | 36.70% | 3.33% | 1.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1209987334 | A -> DEL | LOC_Os12g17420.1 | N | frameshift_variant | Average:54.239; most accessible tissue: Zhenshan97 young leaf, score: 71.497 | N | N | N | N |
| vg1209987334 | A -> T | LOC_Os12g17420.1 | missense_variant ; p.Phe194Tyr; MODERATE | nonsynonymous_codon ; F194Y | Average:54.239; most accessible tissue: Zhenshan97 young leaf, score: 71.497 | unknown | unknown | TOLERATED | 1.00 |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1209987334 | NA | 7.63E-12 | mr1069 | 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 |
| vg1209987334 | NA | 4.43E-06 | mr1075 | 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 |
| vg1209987334 | NA | 5.10E-06 | mr1100 | 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 |
| vg1209987334 | NA | 5.68E-06 | mr1202 | 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 |
| vg1209987334 | NA | 1.46E-09 | mr1864 | 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 |
| vg1209987334 | NA | 2.27E-06 | mr1662_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 |