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Detailed information for vg0502074204:

Variant ID: vg0502074204 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 2074204
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.96, A: 0.04, others allele: 0.00, population size: 108. )

Flanking Sequence (100 bp) in Reference Genome:


CAACATCTACAGCACCAAATTAGTTTCACTATATATGTAACGTTGAATACATTTTTGATAATATCATTGTGTCGTGTTGAAAGTTTTATTATATTTTTCT[G/A]
TAAATTTGATTAAATTAAAAATTAATTTTTGACTATGGAAAAAATTAAAAACGACTCATATTATAAAGAGGGACGAAATTAAACTAATTGTGCTGAATTT

Reverse complement sequence

AAATTCAGCACAATTAGTTTAATTTCGTCCCTCTTTATAATATGAGTCGTTTTTAATTTTTTCCATAGTCAAAAATTAATTTTTAATTTAATCAAATTTA[C/T]
AGAAAAATATAATAAAACTTTCAACACGACACAATGATATTATCAAAAATGTATTCAACGTTACATATATAGTGAAACTAATTTGGTGCTGTAGATGTTG

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 69.50% 30.10% 0.34% 0.00% NA
All Indica  2759 53.40% 46.10% 0.51% 0.00% NA
All Japonica  1512 91.80% 8.20% 0.00% 0.00% NA
Aus  269 98.50% 1.50% 0.00% 0.00% NA
Indica I  595 29.60% 69.60% 0.84% 0.00% NA
Indica II  465 34.00% 65.40% 0.65% 0.00% NA
Indica III  913 83.60% 16.40% 0.00% 0.00% NA
Indica Intermediate  786 47.70% 51.50% 0.76% 0.00% NA
Temperate Japonica  767 98.20% 1.80% 0.00% 0.00% NA
Tropical Japonica  504 83.30% 16.70% 0.00% 0.00% NA
Japonica Intermediate  241 89.20% 10.80% 0.00% 0.00% NA
VI/Aromatic  96 94.80% 4.20% 1.04% 0.00% NA
Intermediate  90 77.80% 21.10% 1.11% 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
vg0502074204 G -> A LOC_Os05g04480.1 upstream_gene_variant ; 3312.0bp to feature; MODIFIER silent_mutation Average:64.19; most accessible tissue: Callus, score: 93.716 N N N N
vg0502074204 G -> A LOC_Os05g04490.1 intron_variant ; MODIFIER silent_mutation Average:64.19; most accessible tissue: Callus, score: 93.716 N N N N

Effects Predicted by Deep Convolutional Neural Networks

For each variant, we constructed two sequences that contain the variation site and the sequence around it, differing only in the variation site. We then used Basenji to predict the chromatin accessibility of each tissue for the two sequences, respectively, and scored the effect of the variant by comparing the changes in chromatin accessibility corresponding to the two genotypes in the 1 kb region around the variation site. The effect score was defined as the logarithmic ratio of the predicted chromatin accessibility of the alternative genotype to the value of the reference genotype.

Var ID Ref Alt Root (RT) Young Leaf (YL) Flag Leaf (FL) Young Panicle (YP) Lemma & Palea (LP) Stamen & Pistil (SP)
vg0502074204 G A 0.02 0.01 -0.01 0.01 -0.01 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0502074204 NA 6.86E-07 mr1179 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
vg0502074204 NA 7.79E-07 mr1624 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
vg0502074204 NA 2.95E-15 mr1807 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
vg0502074204 NA 4.42E-06 mr1838 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
vg0502074204 3.93E-07 6.14E-07 mr1150_2 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