| Variant ID: vg0817475785 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 17475785 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
ACAATTAGCCATGCCAAATTAAATGAACAATTTTTCCAAACACATCTTCTATTATATATATTAAGAAGTTAATTGAACTTCCGACAAGCACTCTTGAGCC[G/A]
CCACGTGACACTCCTACAAACACTCTTAGACCGTCACATAGCTCTATCTAATCTCACCATCGATTTTAACTTAAATTGGTGACCCGATATTTTGGATCAA
TTGATCCAAAATATCGGGTCACCAATTTAAGTTAAAATCGATGGTGAGATTAGATAGAGCTATGTGACGGTCTAAGAGTGTTTGTAGGAGTGTCACGTGG[C/T]
GGCTCAAGAGTGCTTGTCGGAAGTTCAATTAACTTCTTAATATATATAATAGAAGATGTGTTTGGAAAAATTGTTCATTTAATTTGGCATGGCTAATTGT
| 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 | 50.00% | 1.30% | 3.11% | 45.51% | NA |
| All Indica | 2759 | 32.10% | 0.00% | 3.84% | 64.08% | NA |
| All Japonica | 1512 | 77.20% | 3.90% | 2.12% | 16.80% | NA |
| Aus | 269 | 64.70% | 0.00% | 1.12% | 34.20% | NA |
| Indica I | 595 | 51.10% | 0.00% | 5.55% | 43.36% | NA |
| Indica II | 465 | 18.90% | 0.00% | 5.81% | 75.27% | NA |
| Indica III | 913 | 28.40% | 0.00% | 1.10% | 70.54% | NA |
| Indica Intermediate | 786 | 29.80% | 0.00% | 4.58% | 65.65% | NA |
| Temperate Japonica | 767 | 88.70% | 7.20% | 2.87% | 1.30% | NA |
| Tropical Japonica | 504 | 58.10% | 0.00% | 0.99% | 40.87% | NA |
| Japonica Intermediate | 241 | 80.50% | 1.70% | 2.07% | 15.77% | NA |
| VI/Aromatic | 96 | 89.60% | 0.00% | 2.08% | 8.33% | NA |
| Intermediate | 90 | 58.90% | 4.40% | 4.44% | 32.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0817475785 | G -> A | LOC_Os08g28600.1 | intron_variant ; MODIFIER | silent_mutation | Average:16.632; most accessible tissue: Callus, score: 61.54 | N | N | N | N |
| vg0817475785 | G -> DEL | N | N | silent_mutation | Average:16.632; most accessible tissue: Callus, score: 61.54 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0817475785 | NA | 3.56E-08 | mr1712 | Jap_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 |
| vg0817475785 | 2.10E-06 | 2.09E-06 | mr1770 | Jap_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 |