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Detailed information for vg0332031704:

Variant ID: vg0332031704 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 32031704
Reference Allele: GAlternative Allele: A,T
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: 281. )

Flanking Sequence (100 bp) in Reference Genome:


TGTCATTAGCAAATGTTTACTGCAACACCACATTATCAAATCACGACGCAATTAGGTTTAAAAGATTCGTCTCGCAATTTACACACAAACTGTGTAATTG[G/A,T]
TTTTTTTCGTCCGCATTTAATGCTCCATGCATGTGTCCAAGTGTTCGATATGATATGGTGAAAAAATTTTAGGTGGGATTTAAACAGGGCCTAACTTGTG

Reverse complement sequence

CACAAGTTAGGCCCTGTTTAAATCCCACCTAAAATTTTTTCACCATATCATATCGAACACTTGGACACATGCATGGAGCATTAAATGCGGACGAAAAAAA[C/T,A]
CAATTACACAGTTTGTGTGTAAATTGCGAGACGAATCTTTTAAACCTAATTGCGTCGTGATTTGATAATGTGGTGTTGCAGTAAACATTTGCTAATGACA

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 90.90% 8.80% 0.19% 0.00% T: 0.06%
All Indica  2759 99.80% 0.10% 0.00% 0.00% T: 0.04%
All Japonica  1512 73.30% 26.20% 0.46% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.60% 0.20% 0.00% 0.00% T: 0.22%
Indica III  913 99.80% 0.20% 0.00% 0.00% NA
Indica Intermediate  786 99.90% 0.10% 0.00% 0.00% NA
Temperate Japonica  767 99.60% 0.40% 0.00% 0.00% NA
Tropical Japonica  504 22.60% 76.00% 1.39% 0.00% NA
Japonica Intermediate  241 95.90% 4.10% 0.00% 0.00% NA
VI/Aromatic  96 95.80% 4.20% 0.00% 0.00% NA
Intermediate  90 81.10% 14.40% 2.22% 0.00% T: 2.22%

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0332031704 G -> T LOC_Os03g56220.1 upstream_gene_variant ; 1789.0bp to feature; MODIFIER silent_mutation Average:95.158; most accessible tissue: Minghui63 flower, score: 98.465 N N N N
vg0332031704 G -> T LOC_Os03g56234.1 downstream_gene_variant ; 3262.0bp to feature; MODIFIER silent_mutation Average:95.158; most accessible tissue: Minghui63 flower, score: 98.465 N N N N
vg0332031704 G -> T LOC_Os03g56234.2 downstream_gene_variant ; 2961.0bp to feature; MODIFIER silent_mutation Average:95.158; most accessible tissue: Minghui63 flower, score: 98.465 N N N N
vg0332031704 G -> T LOC_Os03g56220-LOC_Os03g56234 intergenic_region ; MODIFIER silent_mutation Average:95.158; most accessible tissue: Minghui63 flower, score: 98.465 N N N N
vg0332031704 G -> A LOC_Os03g56220.1 upstream_gene_variant ; 1789.0bp to feature; MODIFIER silent_mutation Average:95.158; most accessible tissue: Minghui63 flower, score: 98.465 N N N N
vg0332031704 G -> A LOC_Os03g56234.1 downstream_gene_variant ; 3262.0bp to feature; MODIFIER silent_mutation Average:95.158; most accessible tissue: Minghui63 flower, score: 98.465 N N N N
vg0332031704 G -> A LOC_Os03g56234.2 downstream_gene_variant ; 2961.0bp to feature; MODIFIER silent_mutation Average:95.158; most accessible tissue: Minghui63 flower, score: 98.465 N N N N
vg0332031704 G -> A LOC_Os03g56220-LOC_Os03g56234 intergenic_region ; MODIFIER silent_mutation Average:95.158; most accessible tissue: Minghui63 flower, score: 98.465 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)
vg0332031704 G A 0.0 0.01 0.01 0.0 0.0 0.0
vg0332031704 G T 0.01 -0.01 0.0 0.0 0.01 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0332031704 NA 8.33E-09 mr1551 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
vg0332031704 NA 7.93E-07 mr1554 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
vg0332031704 NA 5.46E-07 mr1696 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
vg0332031704 NA 1.23E-11 mr1871 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
vg0332031704 NA 8.36E-13 mr1879 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
vg0332031704 1.37E-07 NA mr1174_2 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
vg0332031704 NA 1.17E-06 mr1174_2 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
vg0332031704 NA 1.24E-09 mr1347_2 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
vg0332031704 NA 1.34E-10 mr1398_2 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
vg0332031704 NA 9.22E-07 mr1398_2 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
vg0332031704 NA 3.08E-08 mr1449_2 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
vg0332031704 NA 2.82E-08 mr1551_2 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
vg0332031704 NA 9.78E-15 mr1552_2 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
vg0332031704 NA 3.18E-08 mr1623_2 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
vg0332031704 NA 4.13E-07 mr1653_2 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
vg0332031704 NA 1.18E-09 mr1696_2 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
vg0332031704 NA 4.84E-08 mr1696_2 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
vg0332031704 NA 1.60E-09 mr1705_2 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
vg0332031704 NA 4.48E-13 mr1742_2 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
vg0332031704 NA 1.45E-07 mr1819_2 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
vg0332031704 NA 3.14E-09 mr1879_2 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
vg0332031704 NA 2.21E-09 mr1905_2 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
vg0332031704 NA 1.11E-06 mr1966_2 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