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Detailed information for vg0320899688:

Variant ID: vg0320899688 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 20899688
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.97, A: 0.03, others allele: 0.00, population size: 119. )

Flanking Sequence (100 bp) in Reference Genome:


GAGGAGAAGCCCGGCAGCCACCTCCGCGAAGACGCAAGCCATCGGAGCACCGTCGTCACCGTGAAGCCGATTTGTTCCATCTTCAGCCGCGCCGTTCGTC[G/A]
CCGTCCATCGCCGCCTTCGTTCACCGTCGCCACCCTCGGGATCGCAGGAGCGAGGTGAAGACCGTCCGCCCCTCGGTTGCTGCCTCTCGTCGCCGGAAAG

Reverse complement sequence

CTTTCCGGCGACGAGAGGCAGCAACCGAGGGGCGGACGGTCTTCACCTCGCTCCTGCGATCCCGAGGGTGGCGACGGTGAACGAAGGCGGCGATGGACGG[C/T]
GACGAACGGCGCGGCTGAAGATGGAACAAATCGGCTTCACGGTGACGACGGTGCTCCGATGGCTTGCGTCTTCGCGGAGGTGGCTGCCGGGCTTCTCCTC

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 61.90% 29.00% 7.11% 1.95% NA
All Indica  2759 38.10% 47.40% 11.49% 3.04% NA
All Japonica  1512 99.30% 0.70% 0.07% 0.00% NA
Aus  269 81.80% 11.90% 4.09% 2.23% NA
Indica I  595 48.40% 30.80% 17.65% 3.19% NA
Indica II  465 32.50% 61.10% 6.02% 0.43% NA
Indica III  913 37.10% 49.20% 9.42% 4.27% NA
Indica Intermediate  786 34.70% 49.70% 12.47% 3.05% NA
Temperate Japonica  767 99.60% 0.40% 0.00% 0.00% NA
Tropical Japonica  504 98.60% 1.20% 0.20% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 96.90% 2.10% 1.04% 0.00% NA
Intermediate  90 67.80% 23.30% 6.67% 2.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0320899688 G -> A LOC_Os03g37670.1 upstream_gene_variant ; 4634.0bp to feature; MODIFIER silent_mutation Average:79.154; most accessible tissue: Zhenshan97 flag leaf, score: 97.091 N N N N
vg0320899688 G -> A LOC_Os03g37680.1 upstream_gene_variant ; 59.0bp to feature; MODIFIER silent_mutation Average:79.154; most accessible tissue: Zhenshan97 flag leaf, score: 97.091 N N N N
vg0320899688 G -> A LOC_Os03g37690.1 upstream_gene_variant ; 2001.0bp to feature; MODIFIER silent_mutation Average:79.154; most accessible tissue: Zhenshan97 flag leaf, score: 97.091 N N N N
vg0320899688 G -> A LOC_Os03g37680-LOC_Os03g37690 intergenic_region ; MODIFIER silent_mutation Average:79.154; most accessible tissue: Zhenshan97 flag leaf, score: 97.091 N N N N
vg0320899688 G -> DEL N N silent_mutation Average:79.154; most accessible tissue: Zhenshan97 flag leaf, score: 97.091 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)
vg0320899688 G A -0.02 -0.03 -0.02 -0.02 -0.02 -0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0320899688 NA 3.86E-08 mr1040 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
vg0320899688 NA 1.02E-06 mr1053 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
vg0320899688 NA 1.84E-07 mr1115 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
vg0320899688 NA 3.41E-07 mr1669 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
vg0320899688 NA 1.28E-07 mr1785 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
vg0320899688 NA 2.55E-08 mr1804 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
vg0320899688 NA 4.88E-06 mr1844 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