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Detailed information for vg0225153266:

Variant ID: vg0225153266 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 25153266
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.98, G: 0.02, others allele: 0.00, population size: 286. )

Flanking Sequence (100 bp) in Reference Genome:


AATCTGCTCCATGACAAATCGCTTTTACTGCGCGTGTACGACGAGCAGTAACAATTGCCTTTAATTACTCTTAATCGTAGTAAAAAATTTTACAGTACAC[G/A]
AATGAAAATGACAGTAATACTAAACAAATATGTCGTGTTTATCATCTTCATTCTCTCGAGAAATAGTACATGTCACGATGAATCAACAACAAGCAGCTAG

Reverse complement sequence

CTAGCTGCTTGTTGTTGATTCATCGTGACATGTACTATTTCTCGAGAGAATGAAGATGATAAACACGACATATTTGTTTAGTATTACTGTCATTTTCATT[C/T]
GTGTACTGTAAAATTTTTTACTACGATTAAGAGTAATTAAAGGCAATTGTTACTGCTCGTCGTACACGCGCAGTAAAAGCGATTTGTCATGGAGCAGATT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 57.60% 42.30% 0.17% 0.00% NA
All Indica  2759 79.10% 20.80% 0.11% 0.00% NA
All Japonica  1512 12.80% 87.00% 0.26% 0.00% NA
Aus  269 93.30% 6.70% 0.00% 0.00% NA
Indica I  595 74.30% 25.70% 0.00% 0.00% NA
Indica II  465 72.00% 28.00% 0.00% 0.00% NA
Indica III  913 90.80% 9.20% 0.00% 0.00% NA
Indica Intermediate  786 73.30% 26.30% 0.38% 0.00% NA
Temperate Japonica  767 4.70% 94.80% 0.52% 0.00% NA
Tropical Japonica  504 24.60% 75.40% 0.00% 0.00% NA
Japonica Intermediate  241 13.70% 86.30% 0.00% 0.00% NA
VI/Aromatic  96 50.00% 50.00% 0.00% 0.00% NA
Intermediate  90 52.20% 46.70% 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
vg0225153266 G -> A LOC_Os02g41840.1 3_prime_UTR_variant ; 347.0bp to feature; MODIFIER silent_mutation Average:92.856; most accessible tissue: Callus, score: 99.337 N N N N
vg0225153266 G -> A LOC_Os02g41820.1 upstream_gene_variant ; 4321.0bp to feature; MODIFIER silent_mutation Average:92.856; most accessible tissue: Callus, score: 99.337 N N N N
vg0225153266 G -> A LOC_Os02g41850.1 upstream_gene_variant ; 3283.0bp to feature; MODIFIER silent_mutation Average:92.856; most accessible tissue: Callus, score: 99.337 N N N N
vg0225153266 G -> A LOC_Os02g41830.1 downstream_gene_variant ; 2160.0bp to feature; MODIFIER silent_mutation Average:92.856; most accessible tissue: Callus, score: 99.337 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)
vg0225153266 G A -0.03 -0.03 -0.05 0.02 -0.01 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0225153266 NA 1.49E-07 mr1190 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
vg0225153266 NA 6.36E-06 mr1192 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
vg0225153266 NA 6.41E-08 mr1646 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
vg0225153266 NA 2.40E-06 mr1871 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
vg0225153266 4.47E-06 NA mr1023_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
vg0225153266 NA 5.95E-06 mr1457_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