Variant ID: vg1217925281 (JBrowse) | Variation Type: SNP |
Chromosome: chr12 | Position: 17925281 |
Reference Allele: C | Alternative Allele: A |
Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 318. )
ACAATGTGCGAATTCCATCTTCCATGATATTAATTATAGGAAAACATTTGGATAAAAAATAACTCATAAACTGATCTTCGTGGTGGATCTGCCACCATCA[C/A]
ATGGCTACTGATATCATAAATATTGACTAGCTTTGCTCACAGGCCAAGCTTATTTGATCAATCCCCCCAGAGTGTCAAACTGAAGGAGACATGAGGAATA
TATTCCTCATGTCTCCTTCAGTTTGACACTCTGGGGGGATTGATCAAATAAGCTTGGCCTGTGAGCAAAGCTAGTCAATATTTATGATATCAGTAGCCAT[G/T]
TGATGGTGGCAGATCCACCACGAAGATCAGTTTATGAGTTATTTTTTATCCAAATGTTTTCCTATAATTAATATCATGGAAGATGGAATTCGCACATTGT
Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 93.80% | 6.10% | 0.04% | 0.00% | NA |
All Indica | 2759 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
All Japonica | 1512 | 82.00% | 18.00% | 0.00% | 0.00% | NA |
Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica I | 595 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica III | 913 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
Indica Intermediate | 786 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
Temperate Japonica | 767 | 90.70% | 9.30% | 0.00% | 0.00% | NA |
Tropical Japonica | 504 | 66.90% | 33.10% | 0.00% | 0.00% | NA |
Japonica Intermediate | 241 | 85.90% | 14.10% | 0.00% | 0.00% | NA |
VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Intermediate | 90 | 85.60% | 12.20% | 2.22% | 0.00% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg1217925281 | C -> A | LOC_Os12g29990.1 | intron_variant ; MODIFIER | silent_mutation | Average:64.95; most accessible tissue: Callus, score: 87.203 | N | N | N | N |
vg1217925281 | C -> A | LOC_Os12g29990.4 | intron_variant ; MODIFIER | silent_mutation | Average:64.95; most accessible tissue: Callus, score: 87.203 | N | N | N | N |
vg1217925281 | C -> A | LOC_Os12g29990.2 | intron_variant ; MODIFIER | silent_mutation | Average:64.95; most accessible tissue: Callus, score: 87.203 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg1217925281 | 1.09E-06 | NA | mr1480 | 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 |
vg1217925281 | 6.04E-06 | 6.04E-06 | mr1480 | Jap_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 |
vg1217925281 | NA | 7.08E-06 | mr1786 | 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 |
vg1217925281 | NA | 5.71E-06 | mr1960 | 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 |