| Variant ID: vg0805526977 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 5526977 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 254. )
CAAATAATGCGCGATGAACCGCTTCATCAACTGTATCTTGAAGTATTTCAACTATCAGCTTGGGGAATCGAGTCTTCTGAATTGGCCCTTCTGGTGTCAT[G/A]
ATGAAACATTGAAGACGACGCATTTGAAAATCAGCTACAAACTGCTCCATCTGTTGCCTCTGTTCCTCCGTTAAATTCTCCACCGTGACCATGATCTTTG
CAAAGATCATGGTCACGGTGGAGAATTTAACGGAGGAACAGAGGCAACAGATGGAGCAGTTTGTAGCTGATTTTCAAATGCGTCGTCTTCAATGTTTCAT[C/T]
ATGACACCAGAAGGGCCAATTCAGAAGACTCGATTCCCCAAGCTGATAGTTGAAATACTTCAAGATACAGTTGATGAAGCGGTTCATCGCGCATTATTTG
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 89.50% | 4.10% | 1.23% | 5.18% | NA |
| All Indica | 2759 | 87.00% | 6.60% | 0.98% | 5.40% | NA |
| All Japonica | 1512 | 93.30% | 0.20% | 1.59% | 4.89% | NA |
| Aus | 269 | 98.10% | 1.10% | 0.00% | 0.74% | NA |
| Indica I | 595 | 99.00% | 0.30% | 0.17% | 0.50% | NA |
| Indica II | 465 | 91.80% | 5.40% | 0.00% | 2.80% | NA |
| Indica III | 913 | 76.30% | 11.00% | 1.86% | 10.84% | NA |
| Indica Intermediate | 786 | 87.40% | 7.10% | 1.15% | 4.33% | NA |
| Temperate Japonica | 767 | 98.80% | 0.00% | 0.91% | 0.26% | NA |
| Tropical Japonica | 504 | 85.90% | 0.60% | 2.38% | 11.11% | NA |
| Japonica Intermediate | 241 | 91.30% | 0.00% | 2.07% | 6.64% | NA |
| VI/Aromatic | 96 | 71.90% | 2.10% | 6.25% | 19.79% | NA |
| Intermediate | 90 | 93.30% | 4.40% | 1.11% | 1.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0805526977 | G -> A | LOC_Os08g09540.1 | synonymous_variant ; p.Ile41Ile; LOW | synonymous_codon | Average:48.272; most accessible tissue: Minghui63 flag leaf, score: 59.912 | N | N | N | N |
| vg0805526977 | G -> DEL | LOC_Os08g09540.1 | N | frameshift_variant | Average:48.272; most accessible tissue: Minghui63 flag leaf, score: 59.912 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0805526977 | 3.01E-07 | 1.97E-06 | mr1096_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 |
| vg0805526977 | NA | 9.65E-07 | mr1111_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 |
| vg0805526977 | 6.90E-08 | 3.07E-07 | mr1121_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 |
| vg0805526977 | 4.38E-06 | 3.65E-08 | mr1144_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 |