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Detailed information for vg0304596104:

Variant ID: vg0304596104 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 4596104
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 122. )

Flanking Sequence (100 bp) in Reference Genome:


AACCGTGGGCCGTCCGATCTGCCACGTCCTCGGACTTTCCCCCCTCTACTCCGCTTCCCTTCCTCTCTCCTTCGTCCTCTCCTCTCCGTTCCAATCCAAG[C/T]
CGCGTCGCTGGGAAATTTGCAGCCTCGATCTCCGCCCGGGAAGACGCGGATCCGGAGGAGGAAAGCAGCATCGGTCTCCATCTCCTCGGGCTCAATCTTT

Reverse complement sequence

AAAGATTGAGCCCGAGGAGATGGAGACCGATGCTGCTTTCCTCCTCCGGATCCGCGTCTTCCCGGGCGGAGATCGAGGCTGCAAATTTCCCAGCGACGCG[G/A]
CTTGGATTGGAACGGAGAGGAGAGGACGAAGGAGAGAGGAAGGGAAGCGGAGTAGAGGGGGGAAAGTCCGAGGACGTGGCAGATCGGACGGCCCACGGTT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 61.00% 38.90% 0.11% 0.00% NA
All Indica  2759 39.70% 60.10% 0.18% 0.00% NA
All Japonica  1512 97.60% 2.40% 0.00% 0.00% NA
Aus  269 55.00% 45.00% 0.00% 0.00% NA
Indica I  595 5.70% 94.10% 0.17% 0.00% NA
Indica II  465 87.10% 12.90% 0.00% 0.00% NA
Indica III  913 32.90% 66.80% 0.33% 0.00% NA
Indica Intermediate  786 45.40% 54.50% 0.13% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 93.10% 6.90% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 95.80% 4.20% 0.00% 0.00% NA
Intermediate  90 81.10% 18.90% 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
vg0304596104 C -> T LOC_Os03g08870.1 5_prime_UTR_variant ; 127.0bp to feature; MODIFIER silent_mutation Average:98.865; most accessible tissue: Minghui63 flower, score: 99.681 N N N N
vg0304596104 C -> T LOC_Os03g08860.1 downstream_gene_variant ; 1193.0bp to feature; MODIFIER silent_mutation Average:98.865; most accessible tissue: Minghui63 flower, score: 99.681 N N N N
vg0304596104 C -> T LOC_Os03g08880.1 downstream_gene_variant ; 2820.0bp to feature; MODIFIER silent_mutation Average:98.865; most accessible tissue: Minghui63 flower, score: 99.681 N N N N
vg0304596104 C -> T LOC_Os03g08860.2 downstream_gene_variant ; 1193.0bp to feature; MODIFIER silent_mutation Average:98.865; most accessible tissue: Minghui63 flower, score: 99.681 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)
vg0304596104 C T -0.17 -0.22 -0.17 -0.13 -0.17 -0.16

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0304596104 NA 2.30E-07 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
vg0304596104 NA 7.06E-07 mr1593 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
vg0304596104 NA 1.78E-12 mr1660 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
vg0304596104 NA 8.51E-08 mr1660 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
vg0304596104 NA 6.48E-06 mr1944 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
vg0304596104 NA 1.16E-09 mr1299_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
vg0304596104 NA 2.31E-06 mr1319_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
vg0304596104 NA 2.37E-08 mr1383_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
vg0304596104 NA 3.10E-08 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
vg0304596104 NA 8.30E-09 mr1593_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
vg0304596104 NA 1.32E-10 mr1660_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
vg0304596104 NA 3.11E-08 mr1700_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
vg0304596104 NA 5.60E-10 mr1715_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
vg0304596104 NA 2.90E-07 mr1727_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
vg0304596104 NA 2.97E-10 mr1756_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
vg0304596104 NA 3.61E-06 mr1876_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
vg0304596104 NA 8.11E-10 mr1946_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
vg0304596104 NA 8.11E-10 mr1948_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
vg0304596104 NA 1.46E-07 mr1977_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