| Variant ID: vg0619641710 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 19641710 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.02, others allele: 0.00, population size: 204. )
CGAAGACGACTTTCTCCTCATCGCTGCACTGCACCGTGTCTAGCTTTTTCCCCACGGCATGCAACCAATCCAACGCATCCACGGGGTTGTTGGAGCTAGA[A/G]
AAGGTAGGTGGGCGGATGCGGAGGAATTCGGCGAGTTTGGAGTGTTGGGGAGGGGGTGGTGGAGCATTCTGTTGTGGCGGATTTTGGAGGTGGTGGAGGA
TCCTCCACCACCTCCAAAATCCGCCACAACAGAATGCTCCACCACCCCCTCCCCAACACTCCAAACTCGCCGAATTCCTCCGCATCCGCCCACCTACCTT[T/C]
TCTAGCTCCAACAACCCCGTGGATGCGTTGGATTGGTTGCATGCCGTGGGGAAAAAGCTAGACACGGTGCAGTGCAGCGATGAGGAGAAAGTCGTCTTCG
| 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 | 30.50% | 8.40% | 27.57% | 33.54% | NA |
| All Indica | 2759 | 4.90% | 5.50% | 39.25% | 50.34% | NA |
| All Japonica | 1512 | 81.10% | 0.80% | 7.01% | 11.11% | NA |
| Aus | 269 | 1.50% | 83.30% | 14.50% | 0.74% | NA |
| Indica I | 595 | 1.80% | 1.80% | 20.00% | 76.30% | NA |
| Indica II | 465 | 4.70% | 1.70% | 24.09% | 69.46% | NA |
| Indica III | 913 | 5.70% | 7.60% | 64.84% | 21.91% | NA |
| Indica Intermediate | 786 | 6.50% | 8.00% | 33.08% | 52.42% | NA |
| Temperate Japonica | 767 | 74.30% | 0.00% | 7.17% | 18.51% | NA |
| Tropical Japonica | 504 | 89.70% | 2.20% | 7.94% | 0.20% | NA |
| Japonica Intermediate | 241 | 84.60% | 0.40% | 4.56% | 10.37% | NA |
| VI/Aromatic | 96 | 30.20% | 7.30% | 55.21% | 7.29% | NA |
| Intermediate | 90 | 51.10% | 3.30% | 24.44% | 21.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0619641710 | A -> G | LOC_Os06g33750.1 | synonymous_variant ; p.Phe212Phe; LOW | synonymous_codon | Average:27.925; most accessible tissue: Minghui63 young leaf, score: 40.718 | N | N | N | N |
| vg0619641710 | A -> DEL | LOC_Os06g33750.1 | N | frameshift_variant | Average:27.925; most accessible tissue: Minghui63 young leaf, score: 40.718 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0619641710 | NA | 3.67E-10 | mr1904 | 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 |
| vg0619641710 | NA | 1.36E-07 | mr1548_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 |
| vg0619641710 | NA | 8.61E-09 | mr1835_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 |
| vg0619641710 | 2.46E-06 | 6.12E-07 | mr1842_2 | 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 |