Variant ID: vg1014702877 (JBrowse) | Variation Type: SNP |
Chromosome: chr10 | Position: 14702877 |
Reference Allele: G | Alternative Allele: T |
Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, T: 0.00, others allele: 0.00, population size: 222. )
TTTTGAATGTGATTGGCAGTGTTTTTAACCTGACTCTGGCAAGAGATATCAAGCATCTTTTAGGAGGTTGGCTTTGTGATTTAATAAAGAAGATAAAAAG[G/T]
TAGTGGTAGTTGGGATTGCTGCTGTTCTTTGGGTTATTTGGAAAGCCAGGAATGCTGCATGCTTTAAAAAGGAAAAATTGAATGACCCGGTGGAACTAAT
ATTAGTTCCACCGGGTCATTCAATTTTTCCTTTTTAAAGCATGCAGCATTCCTGGCTTTCCAAATAACCCAAAGAACAGCAGCAATCCCAACTACCACTA[C/A]
CTTTTTATCTTCTTTATTAAATCACAAAGCCAACCTCCTAAAAGATGCTTGATATCTCTTGCCAGAGTCAGGTTAAAAACACTGCCAATCACATTCAAAA
Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 84.30% | 15.60% | 0.15% | 0.00% | NA |
All Indica | 2759 | 73.30% | 26.50% | 0.25% | 0.00% | NA |
All Japonica | 1512 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica I | 595 | 71.10% | 28.10% | 0.84% | 0.00% | NA |
Indica II | 465 | 87.10% | 12.70% | 0.22% | 0.00% | NA |
Indica III | 913 | 66.60% | 33.30% | 0.11% | 0.00% | NA |
Indica Intermediate | 786 | 74.60% | 25.40% | 0.00% | 0.00% | NA |
Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Tropical Japonica | 504 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
Japonica Intermediate | 241 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Intermediate | 90 | 95.60% | 4.40% | 0.00% | 0.00% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg1014702877 | G -> T | LOC_Os10g28260.1 | splice_donor_variant&intron_variant ; HIGH | splice_donor_variant | Average:51.275; most accessible tissue: Zhenshan97 flower, score: 84.504 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg1014702877 | NA | 2.93E-06 | mr1189 | 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 |
vg1014702877 | NA | 6.22E-06 | mr1346 | 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 |
vg1014702877 | NA | 2.66E-06 | mr1625 | 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 |
vg1014702877 | 4.64E-06 | 4.65E-06 | mr1966 | 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 |
vg1014702877 | 5.07E-06 | 5.07E-06 | mr1966 | 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 |
vg1014702877 | NA | 1.40E-06 | mr1990 | 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 |