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Detailed information for vg0809017868:

Variant ID: vg0809017868 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 9017868
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 120. )

Flanking Sequence (100 bp) in Reference Genome:


TGTTAAGCTTCCCAGGATAAATCGTTTTAACACACTTGCTAACCATTTTGAGGGTATAATACCACCCACCTTCTCAAACGCATCTGCTCTTGAATCCTTG[C/A]
TTCTTCGTGGAAACAACTACCATGGCATTATTCCTAGGGAAATTGGCATCCATGGTAACCTGAAGGTTTTTTCGTTAGGAGACAACGCACTCCAAGCCAC

Reverse complement sequence

GTGGCTTGGAGTGCGTTGTCTCCTAACGAAAAAACCTTCAGGTTACCATGGATGCCAATTTCCCTAGGAATAATGCCATGGTAGTTGTTTCCACGAAGAA[G/T]
CAAGGATTCAAGAGCAGATGCGTTTGAGAAGGTGGGTGGTATTATACCCTCAAAATGGTTAGCAAGTGTGTTAAAACGATTTATCCTGGGAAGCTTAACA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 85.00% 5.10% 0.85% 9.08% NA
All Indica  2759 77.10% 8.50% 1.12% 13.34% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 75.80% 0.70% 3.35% 20.07% NA
Indica I  595 97.60% 0.20% 0.00% 2.18% NA
Indica II  465 67.70% 27.50% 1.51% 3.23% NA
Indica III  913 64.80% 6.10% 1.75% 27.27% NA
Indica Intermediate  786 81.20% 6.20% 1.02% 11.58% 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 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 96.90% 0.00% 0.00% 3.12% NA
Intermediate  90 93.30% 2.20% 0.00% 4.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0809017868 C -> A LOC_Os08g14950.1 missense_variant ; p.Leu305Ile; MODERATE nonsynonymous_codon ; L305N Average:58.206; most accessible tissue: Minghui63 flower, score: 74.733 benign 0.637 TOLERATED 0.15
vg0809017868 C -> DEL LOC_Os08g14950.1 N frameshift_variant Average:58.206; most accessible tissue: Minghui63 flower, score: 74.733 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0809017868 NA 2.61E-08 mr1498_2 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
vg0809017868 NA 5.85E-07 mr1942_2 Ind_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