| Variant ID: vg1127566128 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 27566128 |
| 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: 99. )
ATGATTTACAATCAGACTTGTTTTCTTTCTCTACTTTGTCTCTTAGTGCATTGTCATATTGCTCCACAAATTGCTTAAGTGTGGTTCTAGCATTAACATA[A/G]
CCATCAAAGAAGGCATTCACACTCTCACTCCTTTGCGACGAAGACATTCCAGCCCAAAATGTGTCTTTCACATAAGCCGGCACCCATAATTCCCTGTTAT
ATAACAGGGAATTATGGGTGCCGGCTTATGTGAAAGACACATTTTGGGCTGGAATGTCTTCGTCGCAAAGGAGTGAGAGTGTGAATGCCTTCTTTGATGG[T/C]
TATGTTAATGCTAGAACCACACTTAAGCAATTTGTGGAGCAATATGACAATGCACTAAGAGACAAAGTAGAGAAAGAAAACAAGTCTGATTGTAAATCAT
| 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 | 39.80% | 11.80% | 1.57% | 46.87% | NA |
| All Indica | 2759 | 38.30% | 5.00% | 1.92% | 54.77% | NA |
| All Japonica | 1512 | 44.80% | 20.50% | 0.99% | 33.66% | NA |
| Aus | 269 | 14.90% | 34.20% | 1.49% | 49.44% | NA |
| Indica I | 595 | 49.90% | 3.40% | 1.68% | 45.04% | NA |
| Indica II | 465 | 65.80% | 6.00% | 1.29% | 26.88% | NA |
| Indica III | 913 | 14.50% | 4.20% | 1.97% | 79.41% | NA |
| Indica Intermediate | 786 | 40.80% | 6.70% | 2.42% | 50.00% | NA |
| Temperate Japonica | 767 | 63.40% | 1.60% | 0.91% | 34.16% | NA |
| Tropical Japonica | 504 | 17.90% | 52.20% | 0.60% | 29.37% | NA |
| Japonica Intermediate | 241 | 42.30% | 14.50% | 2.07% | 41.08% | NA |
| VI/Aromatic | 96 | 66.70% | 0.00% | 2.08% | 31.25% | NA |
| Intermediate | 90 | 47.80% | 16.70% | 0.00% | 35.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1127566128 | A -> DEL | LOC_Os11g45530.1 | N | frameshift_variant | Average:21.193; most accessible tissue: Callus, score: 49.594 | N | N | N | N |
| vg1127566128 | A -> G | LOC_Os11g45530.1 | synonymous_variant ; p.Gly424Gly; LOW | synonymous_codon | Average:21.193; most accessible tissue: Callus, score: 49.594 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1127566128 | NA | 6.11E-14 | mr1410 | 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 |
| vg1127566128 | 3.11E-06 | 3.12E-06 | mr1736 | 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 |
| vg1127566128 | NA | 1.55E-14 | mr1410_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 |
| vg1127566128 | NA | 1.83E-11 | mr1410_2 | 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 |
| vg1127566128 | NA | 8.67E-06 | mr1781_2 | 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 |