| Variant ID: vg0402676745 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 2676745 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 259. )
CACCTTGGTCCGTAGTTAATGTTTGCGGAATACTGAACCTATGAATAATATGCTTTAAAATAAAATCAATTACCTCCGTATGAGTCATATTCTTCAAAGG[C/T]
ACGGCTTCGGCCCACTTGGTGAAGTAATCCGTAGCAACTAGCACGAACCTATGCCCCTTTGATGACGAAGGATAAATTTGACCAATGAAATCCAAAACCC
GGGTTTTGGATTTCATTGGTCAAATTTATCCTTCGTCATCAAAGGGGCATAGGTTCGTGCTAGTTGCTACGGATTACTTCACCAAGTGGGCCGAAGCCGT[G/A]
CCTTTGAAGAATATGACTCATACGGAGGTAATTGATTTTATTTTAAAGCATATTATTCATAGGTTCAGTATTCCGCAAACATTAACTACGGACCAAGGTG
| 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 | 46.70% | 12.40% | 7.41% | 33.45% | NA |
| All Indica | 2759 | 37.30% | 13.90% | 9.86% | 38.89% | NA |
| All Japonica | 1512 | 60.00% | 10.90% | 2.78% | 26.32% | NA |
| Aus | 269 | 66.20% | 5.60% | 4.83% | 23.42% | NA |
| Indica I | 595 | 12.80% | 2.50% | 4.37% | 80.34% | NA |
| Indica II | 465 | 44.10% | 5.60% | 12.69% | 37.63% | NA |
| Indica III | 913 | 48.70% | 26.00% | 11.50% | 13.80% | NA |
| Indica Intermediate | 786 | 38.70% | 13.50% | 10.43% | 37.40% | NA |
| Temperate Japonica | 767 | 88.50% | 1.40% | 1.04% | 9.00% | NA |
| Tropical Japonica | 504 | 28.20% | 26.00% | 4.56% | 41.27% | NA |
| Japonica Intermediate | 241 | 35.70% | 9.50% | 4.56% | 50.21% | NA |
| VI/Aromatic | 96 | 51.00% | 15.60% | 17.71% | 15.62% | NA |
| Intermediate | 90 | 48.90% | 8.90% | 6.67% | 35.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0402676745 | C -> DEL | LOC_Os04g05370.1 | N | frameshift_variant | Average:10.826; most accessible tissue: Minghui63 root, score: 19.68 | N | N | N | N |
| vg0402676745 | C -> T | LOC_Os04g05370.1 | synonymous_variant ; p.Val1542Val; LOW | synonymous_codon | Average:10.826; most accessible tissue: Minghui63 root, score: 19.68 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0402676745 | 1.97E-08 | 6.93E-08 | mr1018 | 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 |
| vg0402676745 | 1.03E-06 | 1.68E-06 | mr1136 | 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 |
| vg0402676745 | 6.36E-06 | NA | mr1489 | 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 |
| vg0402676745 | NA | 7.06E-06 | mr1538 | 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 |
| vg0402676745 | 9.34E-06 | 9.34E-06 | mr1778 | 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 |