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Detailed information for vg1224785662:

Variant ID: vg1224785662 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 24785662
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 318. )

Flanking Sequence (100 bp) in Reference Genome:


CTGAAGCCAAAAATATGTTCTACTTATTCATTTTGTTAACAGATAAAGATTATGGAAATTTGTGAATTTTCAACAGGGAAGGAACCTGAAGATCCAAACT[G/A]
TAGCCACTGGCATGTGATTGAGGAAAAGAATACTGATGATGATGAACATGCTGACTACCACTACACGAGGTTTGCCAATTACCTGACTGGCGAGGAACGA

Reverse complement sequence

TCGTTCCTCGCCAGTCAGGTAATTGGCAAACCTCGTGTAGTGGTAGTCAGCATGTTCATCATCATCAGTATTCTTTTCCTCAATCACATGCCAGTGGCTA[C/T]
AGTTTGGATCTTCAGGTTCCTTCCCTGTTGAAAATTCACAAATTTCCATAATCTTTATCTGTTAACAAAATGAATAAGTAGAACATATTTTTGGCTTCAG

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 98.10% 1.30% 0.57% 0.00% NA
All Indica  2759 96.80% 2.20% 0.94% 0.00% NA
All Japonica  1512 99.90% 0.00% 0.07% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 88.40% 8.60% 3.03% 0.00% NA
Indica II  465 99.40% 0.20% 0.43% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 98.10% 1.10% 0.76% 0.00% NA
Temperate Japonica  767 99.90% 0.00% 0.13% 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  90 100.00% 0.00% 0.00% 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
vg1224785662 G -> A LOC_Os12g40090.1 missense_variant ; p.Cys178Tyr; MODERATE nonsynonymous_codon ; C178Y Average:53.591; most accessible tissue: Zhenshan97 panicle, score: 71.253 unknown unknown TOLERATED 0.05

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1224785662 NA 9.89E-13 mr1038 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
vg1224785662 6.35E-06 NA mr1141 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
vg1224785662 4.04E-06 NA mr1158 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
vg1224785662 NA 8.66E-15 mr1389 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
vg1224785662 NA 7.10E-15 mr1038_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
vg1224785662 1.45E-06 2.57E-16 mr1389_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