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Detailed information for vg0628851752:

Variant ID: vg0628851752 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 28851752
Reference Allele: GAlternative Allele: T
Primary Allele: TSecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ACATGTAAGTTACAACGTAATTACACTACGATTGTATTGTAATCATCTGTCAAATTTTTAGGAGAATTTATCGGTAAATATATAGCAAAAATATTTTTTG[G/T]
GGGGGTTTACCATGGTTACCGCGATAATCGGGCTTAGTACGAAGGTGACAACCCCTTCCAAACCATAAAGGGAAACCCTGTGTGTTATTACGGACACTAA

Reverse complement sequence

TTAGTGTCCGTAATAACACACAGGGTTTCCCTTTATGGTTTGGAAGGGGTTGTCACCTTCGTACTAAGCCCGATTATCGCGGTAACCATGGTAAACCCCC[C/A]
CAAAAAATATTTTTGCTATATATTTACCGATAAATTCTCCTAAAAATTTGACAGATGATTACAATACAATCGTAGTGTAATTACGTTGTAACTTACATGT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 54.80% 41.00% 0.57% 3.62% NA
All Indica  2759 90.00% 8.70% 0.43% 0.87% NA
All Japonica  1512 2.70% 97.10% 0.07% 0.13% NA
Aus  269 2.20% 40.50% 4.09% 53.16% NA
Indica I  595 87.70% 11.10% 1.18% 0.00% NA
Indica II  465 89.90% 8.80% 0.22% 1.08% NA
Indica III  913 93.80% 4.60% 0.33% 1.31% NA
Indica Intermediate  786 87.50% 11.50% 0.13% 0.89% NA
Temperate Japonica  767 2.90% 97.10% 0.00% 0.00% NA
Tropical Japonica  504 3.20% 96.60% 0.20% 0.00% NA
Japonica Intermediate  241 1.20% 97.90% 0.00% 0.83% NA
VI/Aromatic  96 7.30% 92.70% 0.00% 0.00% NA
Intermediate  90 56.70% 37.80% 3.33% 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
vg0628851752 G -> T LOC_Os06g47640.1 upstream_gene_variant ; 3730.0bp to feature; MODIFIER silent_mutation Average:81.641; most accessible tissue: Zhenshan97 flag leaf, score: 95.782 N N N N
vg0628851752 G -> T LOC_Os06g47650.1 upstream_gene_variant ; 1619.0bp to feature; MODIFIER silent_mutation Average:81.641; most accessible tissue: Zhenshan97 flag leaf, score: 95.782 N N N N
vg0628851752 G -> T LOC_Os06g47630.1 downstream_gene_variant ; 4816.0bp to feature; MODIFIER silent_mutation Average:81.641; most accessible tissue: Zhenshan97 flag leaf, score: 95.782 N N N N
vg0628851752 G -> T LOC_Os06g47640-LOC_Os06g47650 intergenic_region ; MODIFIER silent_mutation Average:81.641; most accessible tissue: Zhenshan97 flag leaf, score: 95.782 N N N N
vg0628851752 G -> DEL N N silent_mutation Average:81.641; most accessible tissue: Zhenshan97 flag leaf, score: 95.782 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)
vg0628851752 G T -0.01 -0.02 0.0 -0.02 -0.01 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0628851752 NA 2.07E-26 mr1181 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
vg0628851752 NA 2.07E-17 mr1199 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
vg0628851752 NA 7.26E-34 mr1224 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
vg0628851752 NA 2.78E-13 mr1270 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
vg0628851752 NA 1.97E-11 mr1299 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
vg0628851752 NA 2.62E-06 mr1305 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
vg0628851752 NA 2.11E-07 mr1321 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
vg0628851752 NA 1.90E-09 mr1342 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
vg0628851752 9.40E-07 9.40E-07 mr1412 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
vg0628851752 NA 6.29E-25 mr1537 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
vg0628851752 NA 1.00E-25 mr1551 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
vg0628851752 NA 6.07E-19 mr1552 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
vg0628851752 NA 9.68E-06 mr1552 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
vg0628851752 NA 2.41E-18 mr1598 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
vg0628851752 NA 4.57E-18 mr1700 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
vg0628851752 NA 5.02E-10 mr1720 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
vg0628851752 NA 7.50E-06 mr1727 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
vg0628851752 NA 4.90E-32 mr1745 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
vg0628851752 NA 2.67E-08 mr1756 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
vg0628851752 NA 6.33E-49 mr1798 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
vg0628851752 NA 4.32E-07 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
vg0628851752 NA 4.48E-51 mr1063_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
vg0628851752 NA 9.03E-33 mr1161_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
vg0628851752 NA 1.79E-20 mr1183_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
vg0628851752 NA 4.44E-29 mr1932_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