Variant ID: vg1217341046 (JBrowse) | Variation Type: SNP |
Chromosome: chr12 | Position: 17341046 |
Reference Allele: G | Alternative Allele: A |
Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
AGTACTTTGTCCTAAAATGAAGCTATTTTTCTACCTACCTTCTCCTCTCAACCAATCACAACCATTCTTTTTCACCTACTTTCTCTTTTCAACCAATCAC[G/A]
CACCTTCTTTAATCATTCTCACCTACTTTCTTAATACCCGTGCCAACCTCAAAAATGCTTACATTTTGGGACGGAGAAAGTAGTATGGTTGTCAGTTTGA
TCAAACTGACAACCATACTACTTTCTCCGTCCCAAAATGTAAGCATTTTTGAGGTTGGCACGGGTATTAAGAAAGTAGGTGAGAATGATTAAAGAAGGTG[C/T]
GTGATTGGTTGAAAAGAGAAAGTAGGTGAAAAAGAATGGTTGTGATTGGTTGAGAGGAGAAGGTAGGTAGAAAAATAGCTTCATTTTAGGACAAAGTACT
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 | 92.10% | 2.60% | 0.02% | 5.33% | NA |
All Indica | 2759 | 97.10% | 0.10% | 0.00% | 2.83% | NA |
All Japonica | 1512 | 82.80% | 7.70% | 0.07% | 9.39% | NA |
Aus | 269 | 98.10% | 0.00% | 0.00% | 1.86% | NA |
Indica I | 595 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
Indica II | 465 | 91.00% | 0.00% | 0.00% | 9.03% | NA |
Indica III | 913 | 98.50% | 0.00% | 0.00% | 1.53% | NA |
Indica Intermediate | 786 | 97.10% | 0.10% | 0.00% | 2.80% | NA |
Temperate Japonica | 767 | 87.90% | 12.00% | 0.00% | 0.13% | NA |
Tropical Japonica | 504 | 74.20% | 0.20% | 0.20% | 25.40% | NA |
Japonica Intermediate | 241 | 84.60% | 10.00% | 0.00% | 5.39% | NA |
VI/Aromatic | 96 | 78.10% | 0.00% | 0.00% | 21.88% | NA |
Intermediate | 90 | 90.00% | 3.30% | 0.00% | 6.67% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg1217341046 | G -> DEL | N | N | silent_mutation | Average:57.243; most accessible tissue: Zhenshan97 panicle, score: 83.41 | N | N | N | N |
vg1217341046 | G -> A | LOC_Os12g29250-LOC_Os12g29280 | intergenic_region ; MODIFIER | silent_mutation | Average:57.243; most accessible tissue: Zhenshan97 panicle, score: 83.41 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg1217341046 | 4.88E-06 | NA | mr1991_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 |