| Variant ID: vg0805068769 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 5068769 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.92, A: 0.06, others allele: 0.00, population size: 53. )
CCGCGCGCCTTGGTGCCTTGGTGGTGCCGCGGCCACTCTGACCGCCGACTCGCCGCGGCTCCGGTTCATGTCCATCCCCGACGACCACGCGCACGCCATG[G/A]
GCGACATCGTGGAGCTCTTGGAGTCGCTGGGGACCAATGGCAGCCGGGTGAAAGGGGATTGATGCGGTTGGGGCAGGGCCGGCATGACGATCCTCGACAG
CTGTCGAGGATCGTCATGCCGGCCCTGCCCCAACCGCATCAATCCCCTTTCACCCGGCTGCCATTGGTCCCCAGCGACTCCAAGAGCTCCACGATGTCGC[C/T]
CATGGCGTGCGCGTGGTCGTCGGGGATGGACATGAACCGGAGCCGCGGCGAGTCGGCGGTCAGAGTGGCCGCGGCACCACCAAGGCACCAAGGCGCGCGG
| 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 | 33.60% | 24.00% | 1.33% | 41.09% | NA |
| All Indica | 2759 | 52.40% | 10.70% | 1.05% | 35.88% | NA |
| All Japonica | 1512 | 1.10% | 51.80% | 1.46% | 45.63% | NA |
| Aus | 269 | 29.00% | 10.40% | 2.23% | 58.36% | NA |
| Indica I | 595 | 89.90% | 2.50% | 0.17% | 7.39% | NA |
| Indica II | 465 | 23.70% | 32.70% | 0.86% | 42.80% | NA |
| Indica III | 913 | 43.00% | 5.80% | 0.88% | 50.27% | NA |
| Indica Intermediate | 786 | 51.90% | 9.40% | 2.04% | 36.64% | NA |
| Temperate Japonica | 767 | 0.70% | 86.70% | 0.65% | 11.99% | NA |
| Tropical Japonica | 504 | 1.40% | 5.40% | 2.78% | 90.48% | NA |
| Japonica Intermediate | 241 | 2.10% | 37.80% | 1.24% | 58.92% | NA |
| VI/Aromatic | 96 | 19.80% | 9.40% | 0.00% | 70.83% | NA |
| Intermediate | 90 | 31.10% | 21.10% | 6.67% | 41.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0805068769 | G -> A | LOC_Os08g08740.1 | missense_variant ; p.Pro291Leu; MODERATE | nonsynonymous_codon ; P291L | Average:76.211; most accessible tissue: Zhenshan97 young leaf, score: 88.127 | unknown | unknown | DELETERIOUS | 0.00 |
| vg0805068769 | G -> DEL | LOC_Os08g08740.1 | N | frameshift_variant | Average:76.211; most accessible tissue: Zhenshan97 young leaf, score: 88.127 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0805068769 | NA | 1.36E-08 | mr1565 | 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 |
| vg0805068769 | NA | 6.28E-06 | mr1629 | 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 |
| vg0805068769 | NA | 7.35E-07 | mr1942 | 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 |
| vg0805068769 | 3.38E-06 | 3.38E-06 | mr1234_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 |