Variant ID: vg1214380715 (JBrowse) | Variation Type: SNP |
Chromosome: chr12 | Position: 14380715 |
Reference Allele: A | Alternative Allele: G |
Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.85, A: 0.15, others allele: 0.00, population size: 96. )
TTAATTATATTCACCGGAAAAGGATCATGATCAAGCTTCATCTTGGAGCCATCGGTGAACTTCAATCGTCCTTCATCTATGGCCGATTGAACCTGTCGTC[A/G]
AAACACATTGCAATCATTAGTGGAATGAGAATGAGAATCATGCCATTTACAATAAGCTCGACGTTTCAATTCTTCTTGAGATGGTATGATATGGCCTTTA
TAAAGGCCATATCATACCATCTCAAGAAGAATTGAAACGTCGAGCTTATTGTAAATGGCATGATTCTCATTCTCATTCCACTAATGATTGCAATGTGTTT[T/C]
GACGACAGGTTCAATCGGCCATAGATGAAGGACGATTGAAGTTCACCGATGGCTCCAAGATGAAGCTTGATCATGATCCTTTTCCGGTGAATATAATTAA
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 | 26.80% | 12.60% | 1.71% | 58.89% | NA |
All Indica | 2759 | 16.80% | 19.80% | 2.61% | 60.82% | NA |
All Japonica | 1512 | 49.90% | 2.80% | 0.26% | 46.96% | NA |
Aus | 269 | 5.20% | 0.40% | 1.12% | 93.31% | NA |
Indica I | 595 | 22.20% | 1.80% | 1.68% | 74.29% | NA |
Indica II | 465 | 13.80% | 35.30% | 3.87% | 47.10% | NA |
Indica III | 913 | 16.50% | 22.90% | 2.85% | 57.72% | NA |
Indica Intermediate | 786 | 14.80% | 20.60% | 2.29% | 62.34% | NA |
Temperate Japonica | 767 | 79.00% | 5.10% | 0.13% | 15.78% | NA |
Tropical Japonica | 504 | 13.30% | 0.00% | 0.60% | 86.11% | NA |
Japonica Intermediate | 241 | 34.00% | 1.70% | 0.00% | 64.32% | NA |
VI/Aromatic | 96 | 4.20% | 1.00% | 1.04% | 93.75% | NA |
Intermediate | 90 | 35.60% | 3.30% | 1.11% | 60.00% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg1214380715 | A -> DEL | N | N | silent_mutation | Average:6.922; most accessible tissue: Callus, score: 22.25 | N | N | N | N |
vg1214380715 | A -> G | LOC_Os12g25050.1 | intron_variant ; MODIFIER | silent_mutation | Average:6.922; most accessible tissue: Callus, score: 22.25 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg1214380715 | 9.48E-06 | NA | mr1326 | 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 |