| Variant ID: vg0519817077 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 19817077 |
| Reference Allele: A | Alternative Allele: C |
| Primary Allele: A | Secondary Allele: C |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.93, C: 0.06, others allele: 0.00, population size: 122. )
CCATTGACGGAATTTTTTATTTATAATAATTAATAATATTTAAATTAAATAATTAGTAATTCCTTTTGAGTATTTACCAAAATAAGAAGGACGCTATTCT[A/C]
AACAGCTTCCGCATCAGGACGCTCCTGTAAACAGCGTCCGCGGATGGACGCTAATCCAAACGACGTCCAGACCGGTGTAGCCACTTCAAATGCAGCGAAC
GTTCGCTGCATTTGAAGTGGCTACACCGGTCTGGACGTCGTTTGGATTAGCGTCCATCCGCGGACGCTGTTTACAGGAGCGTCCTGATGCGGAAGCTGTT[T/G]
AGAATAGCGTCCTTCTTATTTTGGTAAATACTCAAAAGGAATTACTAATTATTTAATTTAAATATTATTAATTATTATAAATAAAAAATTCCGTCAATGG
| Populations | Population Size | Frequency of A(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 75.90% | 23.90% | 0.23% | 0.00% | NA |
| All Indica | 2759 | 60.60% | 39.10% | 0.29% | 0.00% | NA |
| All Japonica | 1512 | 99.10% | 0.90% | 0.00% | 0.00% | NA |
| Aus | 269 | 91.40% | 7.80% | 0.74% | 0.00% | NA |
| Indica I | 595 | 40.20% | 59.80% | 0.00% | 0.00% | NA |
| Indica II | 465 | 59.60% | 39.80% | 0.65% | 0.00% | NA |
| Indica III | 913 | 67.80% | 32.10% | 0.11% | 0.00% | NA |
| Indica Intermediate | 786 | 68.20% | 31.30% | 0.51% | 0.00% | NA |
| Temperate Japonica | 767 | 99.20% | 0.80% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 98.80% | 1.20% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.20% | 0.80% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 83.30% | 15.60% | 1.11% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0519817077 | A -> C | LOC_Os05g33670.1 | upstream_gene_variant ; 3887.0bp to feature; MODIFIER | silent_mutation | Average:46.956; most accessible tissue: Minghui63 panicle, score: 76.913 | N | N | N | N |
| vg0519817077 | A -> C | LOC_Os05g33680.1 | intron_variant ; MODIFIER | silent_mutation | Average:46.956; most accessible tissue: Minghui63 panicle, score: 76.913 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0519817077 | NA | 2.04E-10 | mr1322_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 |
| vg0519817077 | NA | 1.14E-06 | mr1322_2 | 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 |
| vg0519817077 | NA | 4.39E-06 | mr1326_2 | 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 |