| Variant ID: vg0707895416 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 7895416 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, others allele: 0.00, population size: 126. )
ACAAGAGGGGAAGAAGGAGGAGAAGGCTGCCAAAGGGATAAATGTTAGATATAATCAGCCCAAGTCAGTTAATGAGATGATAGAAGTATCTTACTGGTGG[A/G]
GCTGGTTTAGGGGCTAGAGTAACCGATTTCTTCCTCACAGCAATTTTCTTTCTCTATATTTATTAAAATTGTGAGGAATCGGCTATAAAGTAAATGATTG
CAATCATTTACTTTATAGCCGATTCCTCACAATTTTAATAAATATAGAGAAAGAAAATTGCTGTGAGGAAGAAATCGGTTACTCTAGCCCCTAAACCAGC[T/C]
CCACCAGTAAGATACTTCTATCATCTCATTAACTGACTTGGGCTGATTATATCTAACATTTATCCCTTTGGCAGCCTTCTCCTCCTTCTTCCCCTCTTGT
| 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 | 48.30% | 2.40% | 45.11% | 4.15% | NA |
| All Indica | 2759 | 19.00% | 4.10% | 70.53% | 6.38% | NA |
| All Japonica | 1512 | 95.80% | 0.00% | 3.64% | 0.60% | NA |
| Aus | 269 | 59.90% | 0.40% | 38.66% | 1.12% | NA |
| Indica I | 595 | 11.60% | 4.20% | 75.29% | 8.91% | NA |
| Indica II | 465 | 21.50% | 4.70% | 66.02% | 7.74% | NA |
| Indica III | 913 | 14.20% | 4.20% | 76.56% | 5.04% | NA |
| Indica Intermediate | 786 | 28.50% | 3.70% | 62.60% | 5.22% | NA |
| Temperate Japonica | 767 | 99.20% | 0.00% | 0.39% | 0.39% | NA |
| Tropical Japonica | 504 | 89.50% | 0.00% | 9.92% | 0.60% | NA |
| Japonica Intermediate | 241 | 97.90% | 0.00% | 0.83% | 1.24% | NA |
| VI/Aromatic | 96 | 99.00% | 0.00% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 62.20% | 0.00% | 28.89% | 8.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0707895416 | A -> DEL | LOC_Os07g13760.1 | N | frameshift_variant | Average:10.089; most accessible tissue: Callus, score: 23.91 | N | N | N | N |
| vg0707895416 | A -> G | LOC_Os07g13760.1 | synonymous_variant ; p.Ala544Ala; LOW | synonymous_codon | Average:10.089; most accessible tissue: Callus, score: 23.91 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0707895416 | NA | 3.91E-08 | mr1045 | 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 |
| vg0707895416 | NA | 1.46E-12 | mr1169 | 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 |
| vg0707895416 | NA | 6.46E-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 |
| vg0707895416 | NA | 1.78E-09 | mr1342 | 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 |
| vg0707895416 | NA | 3.45E-08 | mr1827 | 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 |
| vg0707895416 | NA | 1.03E-17 | mr1131_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 |
| vg0707895416 | NA | 3.25E-10 | mr1212_2 | 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 |