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Detailed information for vg1220123744:

Variant ID: vg1220123744 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 20123744
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 73. )

Flanking Sequence (100 bp) in Reference Genome:


GACCATGAGAGCTTCCAGAGCCTGATCAACAAAGTCATTAGGCTGGAGAACGATCAAAGGACTGTAGAGCACAACCGCAAGAGGAGGCTTGCTATGAATC[G/A]
CCCACCTCAGGGACCTCAGCGACTCAAGGGAGCCACTTCGTCTGGGTGGAAGCCCCCTATTGTGGCAACCAACCGTCCCGCCGCGCCTAGCAATTTCAAC

Reverse complement sequence

GTTGAAATTGCTAGGCGCGGCGGGACGGTTGGTTGCCACAATAGGGGGCTTCCACCCAGACGAAGTGGCTCCCTTGAGTCGCTGAGGTCCCTGAGGTGGG[C/T]
GATTCATAGCAAGCCTCCTCTTGCGGTTGTGCTCTACAGTCCTTTGATCGTTCTCCAGCCTAATGACTTTGTTGATCAGGCTCTGGAAGCTCTCATGGTC

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 24.30% 3.00% 22.32% 50.36% NA
All Indica  2759 3.50% 4.80% 31.32% 60.42% NA
All Japonica  1512 64.30% 0.00% 0.66% 35.05% NA
Aus  269 15.60% 4.10% 54.28% 26.02% NA
Indica I  595 3.90% 4.00% 26.39% 65.71% NA
Indica II  465 4.70% 4.30% 23.23% 67.74% NA
Indica III  913 2.40% 5.90% 37.90% 53.78% NA
Indica Intermediate  786 3.70% 4.30% 32.19% 59.80% NA
Temperate Japonica  767 93.20% 0.00% 0.26% 6.52% NA
Tropical Japonica  504 22.00% 0.00% 1.19% 76.79% NA
Japonica Intermediate  241 60.60% 0.00% 0.83% 38.59% NA
VI/Aromatic  96 4.20% 0.00% 13.54% 82.29% NA
Intermediate  90 37.80% 0.00% 24.44% 37.78% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1220123744 G -> DEL LOC_Os12g33260.1 N frameshift_variant Average:17.406; most accessible tissue: Callus, score: 36.547 N N N N
vg1220123744 G -> A LOC_Os12g33260.1 missense_variant ; p.Arg479His; MODERATE nonsynonymous_codon ; R479H Average:17.406; most accessible tissue: Callus, score: 36.547 unknown unknown DELETERIOUS 0.05

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1220123744 NA 9.00E-06 mr1029 Jap_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
vg1220123744 NA 4.95E-07 mr1047 Jap_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
vg1220123744 7.54E-06 7.54E-06 mr1189 Jap_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
vg1220123744 NA 4.85E-06 mr1625 Jap_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
vg1220123744 NA 4.25E-07 mr1642 Jap_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
vg1220123744 2.92E-06 2.92E-06 mr1796 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
vg1220123744 NA 9.05E-07 mr1837 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