Variant ID: vg1126395505 (JBrowse) | Variation Type: SNP |
Chromosome: chr11 | Position: 26395505 |
Reference Allele: A | Alternative Allele: G |
Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.52, G: 0.48, others allele: 0.00, population size: 105. )
GTCATCGTTGCGGTGAGCGTCGTTATCCTGTTCCACCCACCTGGCGGAGTTTGGAGTGGCTCTCCTCAGCCCCCGTCACCGCACTGACCCGAGGGTCCCG[A/G]
TGGTCCATAGCCTCCGTGTCATCGTCGTTGCGGGCACTGTCATCGCGAGCGGTCGTCATCATCGCGTAACACCCGCCGGGCGAAGCTCGGAGTGGCTCTC
GAGAGCCACTCCGAGCTTCGCCCGGCGGGTGTTACGCGATGATGACGACCGCTCGCGATGACAGTGCCCGCAACGACGATGACACGGAGGCTATGGACCA[T/C]
CGGGACCCTCGGGTCAGTGCGGTGACGGGGGCTGAGGAGAGCCACTCCAAACTCCGCCAGGTGGGTGGAACAGGATAACGACGCTCACCGCAACGATGAC
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 | 56.70% | 43.00% | 0.21% | 0.00% | NA |
All Indica | 2759 | 38.60% | 61.10% | 0.33% | 0.00% | NA |
All Japonica | 1512 | 86.30% | 13.60% | 0.07% | 0.00% | NA |
Aus | 269 | 57.20% | 42.80% | 0.00% | 0.00% | NA |
Indica I | 595 | 49.40% | 50.60% | 0.00% | 0.00% | NA |
Indica II | 465 | 50.50% | 48.60% | 0.86% | 0.00% | NA |
Indica III | 913 | 19.90% | 80.10% | 0.00% | 0.00% | NA |
Indica Intermediate | 786 | 45.00% | 54.30% | 0.64% | 0.00% | NA |
Temperate Japonica | 767 | 92.30% | 7.60% | 0.13% | 0.00% | NA |
Tropical Japonica | 504 | 81.00% | 19.00% | 0.00% | 0.00% | NA |
Japonica Intermediate | 241 | 78.40% | 21.60% | 0.00% | 0.00% | NA |
VI/Aromatic | 96 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
Intermediate | 90 | 70.00% | 30.00% | 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 |
---|---|---|---|---|---|---|---|---|---|
vg1126395505 | A -> G | LOC_Os11g43710.1 | synonymous_variant ; p.His20His; LOW | synonymous_codon | Average:68.697; most accessible tissue: Zhenshan97 young leaf, score: 88.878 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg1126395505 | NA | 1.38E-06 | mr1121 | Jap_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 |
vg1126395505 | NA | 6.15E-08 | mr1191_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 |
vg1126395505 | NA | 1.53E-06 | mr1662_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 |