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Detailed information for vg1003311148:

Variant ID: vg1003311148 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 3311148
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.94, G: 0.04, others allele: 0.00, population size: 49. )

Flanking Sequence (100 bp) in Reference Genome:


TAGAGGGTCCCTTCTATGAGCACGTATCGCTTAGAGACACGCGTGAGCTTCTCAGCTTCTGCGTGATCCTCAGGAAGAGTATTATTATCGAGATACGCCC[A/G]
AATGTCAGTCAACCAAACGACCTGACGAGGGGGGTTGGGGTCGACCCCCTCGGGCCCCGAGGGCCGCGGGTCGTTAGGGGTCGGGGCGGAGGCCGTGGCG

Reverse complement sequence

CGCCACGGCCTCCGCCCCGACCCCTAACGACCCGCGGCCCTCGGGGCCCGAGGGGGTCGACCCCAACCCCCCTCGTCAGGTCGTTTGGTTGACTGACATT[T/C]
GGGCGTATCTCGATAATAATACTCTTCCTGAGGATCACGCAGAAGCTGAGAAGCTCACGCGTGTCTCTAAGCGATACGTGCTCATAGAAGGGACCCTCTA

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 59.20% 11.00% 0.63% 29.20% NA
All Indica  2759 35.80% 15.20% 1.01% 48.02% NA
All Japonica  1512 97.20% 2.10% 0.07% 0.60% NA
Aus  269 88.80% 8.20% 0.00% 2.97% NA
Indica I  595 49.60% 16.10% 0.50% 33.78% NA
Indica II  465 47.50% 14.20% 0.86% 37.42% NA
Indica III  913 18.30% 16.00% 0.88% 64.84% NA
Indica Intermediate  786 38.80% 14.00% 1.65% 45.55% NA
Temperate Japonica  767 99.60% 0.00% 0.00% 0.39% NA
Tropical Japonica  504 92.50% 6.30% 0.00% 1.19% NA
Japonica Intermediate  241 99.60% 0.00% 0.41% 0.00% NA
VI/Aromatic  96 38.50% 38.50% 0.00% 22.92% NA
Intermediate  90 68.90% 12.20% 1.11% 17.78% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1003311148 A -> G LOC_Os10g06430.1 upstream_gene_variant ; 4611.0bp to feature; MODIFIER silent_mutation Average:43.899; most accessible tissue: Zhenshan97 flag leaf, score: 86.673 N N N N
vg1003311148 A -> G LOC_Os10g06440.1 upstream_gene_variant ; 2213.0bp to feature; MODIFIER silent_mutation Average:43.899; most accessible tissue: Zhenshan97 flag leaf, score: 86.673 N N N N
vg1003311148 A -> G LOC_Os10g06430-LOC_Os10g06440 intergenic_region ; MODIFIER silent_mutation Average:43.899; most accessible tissue: Zhenshan97 flag leaf, score: 86.673 N N N N
vg1003311148 A -> DEL N N silent_mutation Average:43.899; most accessible tissue: Zhenshan97 flag leaf, score: 86.673 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)
vg1003311148 A G 0.0 0.0 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
vg1003311148 7.42E-07 2.23E-08 mr1538 Ind_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
vg1003311148 3.34E-08 4.98E-07 mr1547 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
vg1003311148 3.22E-09 6.66E-11 mr1547 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
vg1003311148 6.82E-11 8.27E-14 mr1709 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
vg1003311148 3.06E-11 8.44E-12 mr1709 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
vg1003311148 NA 8.31E-06 mr1015_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
vg1003311148 NA 9.52E-08 mr1538_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
vg1003311148 4.33E-08 4.66E-11 mr1547_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
vg1003311148 8.66E-10 5.92E-13 mr1547_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
vg1003311148 6.85E-15 4.55E-13 mr1709_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
vg1003311148 1.29E-12 6.07E-12 mr1709_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