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Detailed information for vg0434644596:

Variant ID: vg0434644596 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 34644596
Reference Allele: TAlternative Allele: A
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 336. )

Flanking Sequence (100 bp) in Reference Genome:


GTGTAATTTGGGGATCGATGTGTTGTTTGTCTTGTGAGCCTTGTGAATCCTTTCCCTGTTCTTGTGTCAGAATTCAGAAACGGAACATACGCACGTACCT[T/A]
AACTTTTTTTCCTTACTTTCTGTTCATAATTCAGAGACTGATCTGGATCTGTTCTTCATCGTGTTGTGTTGATCCTGCGACACAAAGACCTGTAAACGTA

Reverse complement sequence

TACGTTTACAGGTCTTTGTGTCGCAGGATCAACACAACACGATGAAGAACAGATCCAGATCAGTCTCTGAATTATGAACAGAAAGTAAGGAAAAAAAGTT[A/T]
AGGTACGTGCGTATGTTCCGTTTCTGAATTCTGACACAAGAACAGGGAAAGGATTCACAAGGCTCACAAGACAAACAACACATCGATCCCCAAATTACAC

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 87.70% 12.10% 0.11% 0.00% NA
All Indica  2759 79.50% 20.30% 0.18% 0.00% NA
All Japonica  1512 99.80% 0.20% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 95.50% 4.50% 0.00% 0.00% NA
Indica II  465 51.20% 48.40% 0.43% 0.00% NA
Indica III  913 82.40% 17.50% 0.11% 0.00% NA
Indica Intermediate  786 80.90% 18.80% 0.25% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.20% 0.80% 0.00% 0.00% NA
VI/Aromatic  96 96.90% 3.10% 0.00% 0.00% NA
Intermediate  90 91.10% 8.90% 0.00% 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
vg0434644596 T -> A LOC_Os04g58160.1 3_prime_UTR_variant ; 372.0bp to feature; MODIFIER silent_mutation Average:82.65; most accessible tissue: Zhenshan97 root, score: 91.211 N N N N
vg0434644596 T -> A LOC_Os04g58160.3 3_prime_UTR_variant ; 372.0bp to feature; MODIFIER silent_mutation Average:82.65; most accessible tissue: Zhenshan97 root, score: 91.211 N N N N
vg0434644596 T -> A LOC_Os04g58160.2 3_prime_UTR_variant ; 372.0bp to feature; MODIFIER silent_mutation Average:82.65; most accessible tissue: Zhenshan97 root, score: 91.211 N N N N
vg0434644596 T -> A LOC_Os04g58180.1 upstream_gene_variant ; 4944.0bp to feature; MODIFIER silent_mutation Average:82.65; most accessible tissue: Zhenshan97 root, score: 91.211 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)
vg0434644596 T A 0.0 0.0 0.0 -0.03 -0.01 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0434644596 NA 4.78E-07 mr1044 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
vg0434644596 NA 2.95E-06 mr1072 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
vg0434644596 NA 5.75E-07 mr1075 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
vg0434644596 NA 2.05E-06 mr1077 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
vg0434644596 NA 7.60E-06 mr1114 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
vg0434644596 NA 3.50E-06 mr1149 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
vg0434644596 NA 6.43E-06 mr1202 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
vg0434644596 NA 5.65E-08 mr1231 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
vg0434644596 NA 1.11E-06 mr1441 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
vg0434644596 NA 1.94E-09 mr1557 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
vg0434644596 NA 2.63E-11 mr1565 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
vg0434644596 NA 1.58E-09 mr1565 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
vg0434644596 NA 5.83E-07 mr1598 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
vg0434644596 9.04E-06 9.04E-06 mr1770 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
vg0434644596 3.20E-06 3.20E-06 mr1955 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
vg0434644596 NA 1.81E-07 mr1295_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
vg0434644596 NA 8.64E-06 mr1295_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
vg0434644596 NA 3.21E-06 mr1482_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
vg0434644596 NA 3.73E-09 mr1557_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
vg0434644596 NA 3.34E-11 mr1598_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