Variant ID: vg0203895379 (JBrowse) | Variation Type: SNP |
Chromosome: chr02 | Position: 3895379 |
Reference Allele: G | Alternative Allele: A |
Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.00, others allele: 0.00, population size: 227. )
TGCAACATTGCTTCAAAATCCTTCTTCTGCTCAGGTGTGAATTTCTCTGGATCGATAGGCACGACGTTTCCTTCATTGATGTCAGTCAACCCCAACTTCT[G/A]
GATCTTTTCTTTAACAGTGCTTGGGCTAGCCGAGGATGGCGACAGCGGTGGCTTCTCGGCCATGAGGAAGAATTGCTTGCTGACTTCTAATTGGTCCCAC
GTGGGACCAATTAGAAGTCAGCAAGCAATTCTTCCTCATGGCCGAGAAGCCACCGCTGTCGCCATCCTCGGCTAGCCCAAGCACTGTTAAAGAAAAGATC[C/T]
AGAAGTTGGGGTTGACTGACATCAATGAAGGAAACGTCGTGCCTATCGATCCAGAGAAATTCACACCTGAGCAGAAGAAGGATTTTGAAGCAATGTTGCA
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 | 96.50% | 3.10% | 0.42% | 0.00% | NA |
All Indica | 2759 | 98.00% | 1.80% | 0.25% | 0.00% | NA |
All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Aus | 269 | 59.10% | 36.40% | 4.46% | 0.00% | NA |
Indica I | 595 | 99.20% | 0.70% | 0.17% | 0.00% | NA |
Indica II | 465 | 97.00% | 2.40% | 0.65% | 0.00% | NA |
Indica III | 913 | 98.00% | 1.90% | 0.11% | 0.00% | NA |
Indica Intermediate | 786 | 97.60% | 2.20% | 0.25% | 0.00% | NA |
Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Intermediate | 90 | 98.90% | 0.00% | 1.11% | 0.00% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0203895379 | G -> A | LOC_Os02g07520.1 | stop_gained ; p.Gln22*; HIGH | stop_gained | Average:39.399; most accessible tissue: Zhenshan97 flag leaf, score: 56.01 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0203895379 | NA | 5.99E-06 | mr1011 | 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 |
vg0203895379 | 2.05E-06 | 2.04E-06 | mr1012 | 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 |