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Detailed information for vg0809872000:

Variant ID: vg0809872000 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 9872000
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.01, others allele: 0.00, population size: 117. )

Flanking Sequence (100 bp) in Reference Genome:


TCCCACCACAGTTCAAGTTCCCACCCGTCCCGCGCTATTCAGGCGAAACTGACCCGAAGAACAGACCGTGCGGTCAAAGCTGTGATGGCGGTCGAAGAAG[T/C]
GCAAGCCCTCCGCAAGGAGTTCGATGCCCAGCAAGCGAGCAACCATCAGCAGCCAGCCCGCAAGAAGGTCCGAAAAGACCTCTACTGCGCCTTTCACGAA

Reverse complement sequence

TTCGTGAAAGGCGCAGTAGAGGTCTTTTCGGACCTTCTTGCGGGCTGGCTGCTGATGGTTGCTCGCTTGCTGGGCATCGAACTCCTTGCGGAGGGCTTGC[A/G]
CTTCTTCGACCGCCATCACAGCTTTGACCGCACGGTCTGTTCTTCGGGTCAGTTTCGCCTGAATAGCGCGGGACGGGTGGGAACTTGAACTGTGGTGGGA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 90.90% 5.70% 2.05% 1.35% NA
All Indica  2759 84.90% 9.40% 3.41% 2.32% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 98.50% 1.10% 0.37% 0.00% NA
Indica I  595 95.80% 1.80% 1.68% 0.67% NA
Indica II  465 91.80% 5.40% 1.29% 1.51% NA
Indica III  913 73.60% 17.40% 4.93% 4.05% NA
Indica Intermediate  786 85.60% 8.10% 4.20% 2.04% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.60% 0.40% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 94.40% 3.30% 2.22% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0809872000 T -> C LOC_Os08g16190.1 missense_variant ; p.Val377Ala; MODERATE nonsynonymous_codon ; V377A Average:45.738; most accessible tissue: Zhenshan97 flag leaf, score: 72.012 benign 0.674 TOLERATED 0.24
vg0809872000 T -> DEL LOC_Os08g16190.1 N frameshift_variant Average:45.738; most accessible tissue: Zhenshan97 flag leaf, score: 72.012 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0809872000 NA 1.41E-08 mr1841 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
vg0809872000 3.76E-07 3.76E-07 mr1900 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