| Variant ID: vg1204294640 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 4294640 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 72. )
GAGGGTGAGAAACCGAGGCGAAGCATTTCTTGACTCCTAGTCCGATGCAATAATCTTGAAAATCGGCGCTGATGAATTGGGAGCCGTTATCCGTTATGAT[A/G]
CGGTGAGGCAATCCATATCGGCAAAATATCCCCTTAATGAACTTGATGGCGTTGTCGGCCTTGATTTCTCCTGTGGGTGTTGCCTCGATCCATTTGGTGA
TCACCAAATGGATCGAGGCAACACCCACAGGAGAAATCAAGGCCGACAACGCCATCAAGTTCATTAAGGGGATATTTTGCCGATATGGATTGCCTCACCG[T/C]
ATCATAACGGATAACGGCTCCCAATTCATCAGCGCCGATTTTCAAGATTATTGCATCGGACTAGGAGTCAAGAAATGCTTCGCCTCGGTTTCTCACCCTC
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 23.70% | 4.00% | 4.00% | 68.37% | NA |
| All Indica | 2759 | 5.90% | 1.30% | 1.34% | 91.45% | NA |
| All Japonica | 1512 | 55.80% | 4.60% | 5.75% | 33.86% | NA |
| Aus | 269 | 24.90% | 25.30% | 18.59% | 31.23% | NA |
| Indica I | 595 | 7.10% | 0.30% | 1.18% | 91.43% | NA |
| Indica II | 465 | 7.70% | 0.90% | 0.86% | 90.54% | NA |
| Indica III | 913 | 1.20% | 2.10% | 1.20% | 95.51% | NA |
| Indica Intermediate | 786 | 9.30% | 1.50% | 1.91% | 87.28% | NA |
| Temperate Japonica | 767 | 80.40% | 0.80% | 1.43% | 17.34% | NA |
| Tropical Japonica | 504 | 28.00% | 8.70% | 11.11% | 52.18% | NA |
| Japonica Intermediate | 241 | 35.70% | 7.90% | 8.30% | 48.13% | NA |
| VI/Aromatic | 96 | 15.60% | 10.40% | 12.50% | 61.46% | NA |
| Intermediate | 90 | 33.30% | 4.40% | 3.33% | 58.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1204294640 | A -> DEL | LOC_Os12g08450.1 | N | frameshift_variant | Average:9.876; most accessible tissue: Zhenshan97 young leaf, score: 20.224 | N | N | N | N |
| vg1204294640 | A -> G | LOC_Os12g08450.1 | synonymous_variant ; p.Arg510Arg; LOW | synonymous_codon | Average:9.876; most accessible tissue: Zhenshan97 young leaf, score: 20.224 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1204294640 | NA | 4.09E-06 | mr1692 | 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 |
| vg1204294640 | NA | 1.05E-06 | mr1781 | 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 |
| vg1204294640 | NA | 2.53E-06 | mr1881 | 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 |
| vg1204294640 | 6.15E-06 | NA | mr1608_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 |
| vg1204294640 | 2.26E-06 | NA | mr1817_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 |