| Variant ID: vg0402237327 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 2237327 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.81, A: 0.19, others allele: 0.00, population size: 90. )
ATGTAATTGAGTTGCAATCTAACTTGTTCTTGCTAGTGTTTTTCGATTCATATGCAGAGATTAGCCTTCTCGGCAAGATCAACCAGGTTTCAGCACGGTT[G/A]
ATAACCAAAGGAGACGTGGTGTTGCGATTGCAGGGTTCGGATCGTGCTGATTGGAAGCCCAATCGTGTGTGTCAAGTTTCCACTAAATCTAGAGTTATCA
TGATAACTCTAGATTTAGTGGAAACTTGACACACACGATTGGGCTTCCAATCAGCACGATCCGAACCCTGCAATCGCAACACCACGTCTCCTTTGGTTAT[C/T]
AACCGTGCTGAAACCTGGTTGATCTTGCCGAGAAGGCTAATCTCTGCATATGAATCGAAAAACACTAGCAAGAACAAGTTAGATTGCAACTCAATTACAT
| 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 | 56.10% | 30.90% | 1.10% | 11.83% | NA |
| All Indica | 2759 | 75.80% | 14.70% | 0.58% | 8.92% | NA |
| All Japonica | 1512 | 16.30% | 65.70% | 1.98% | 16.01% | NA |
| Aus | 269 | 83.60% | 7.40% | 0.74% | 8.18% | NA |
| Indica I | 595 | 93.30% | 5.20% | 0.00% | 1.51% | NA |
| Indica II | 465 | 95.50% | 3.40% | 0.22% | 0.86% | NA |
| Indica III | 913 | 58.10% | 24.30% | 0.44% | 17.20% | NA |
| Indica Intermediate | 786 | 71.50% | 17.40% | 1.40% | 9.67% | NA |
| Temperate Japonica | 767 | 1.70% | 93.70% | 1.83% | 2.74% | NA |
| Tropical Japonica | 504 | 41.10% | 30.80% | 1.59% | 26.59% | NA |
| Japonica Intermediate | 241 | 11.20% | 49.40% | 3.32% | 36.10% | NA |
| VI/Aromatic | 96 | 34.40% | 16.70% | 3.12% | 45.83% | NA |
| Intermediate | 90 | 63.30% | 30.00% | 1.11% | 5.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0402237327 | G -> DEL | LOC_Os04g04650.1 | N | frameshift_variant | Average:33.615; most accessible tissue: Zhenshan97 young leaf, score: 51.997 | N | N | N | N |
| vg0402237327 | G -> A | LOC_Os04g04650.1 | synonymous_variant ; p.Leu32Leu; LOW | synonymous_codon | Average:33.615; most accessible tissue: Zhenshan97 young leaf, score: 51.997 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0402237327 | NA | 2.70E-06 | mr1285 | 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 |
| vg0402237327 | NA | 3.28E-09 | mr1785 | 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 |
| vg0402237327 | NA | 4.89E-06 | mr1872 | 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 |
| vg0402237327 | NA | 2.20E-06 | mr1892 | 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 |
| vg0402237327 | NA | 1.17E-07 | mr1915 | 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 |