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Detailed information for vg0424200736:

Variant ID: vg0424200736 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 24200736
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.95, A: 0.04, others allele: 0.00, population size: 107. )

Flanking Sequence (100 bp) in Reference Genome:


CTTCCCTCGAGAAGCTCAGGTCCAGGCGGCGGATGTCGTGCCGGCTCTCGCGCGACAGGAGGCTCTGCACCGCGCCCACCATCGCGTAGTTGTTCCTCGC[G/A]
GCGTCGGATAGCGTGGAGGTGAAGCCGTCGTCGTCGTGCTCGAAGGAGGAGTCGACGTCCAGCTTGATGTTGGGGAGCATGCCGGGGACGCGCCTCCACC

Reverse complement sequence

GGTGGAGGCGCGTCCCCGGCATGCTCCCCAACATCAAGCTGGACGTCGACTCCTCCTTCGAGCACGACGACGACGGCTTCACCTCCACGCTATCCGACGC[C/T]
GCGAGGAACAACTACGCGATGGTGGGCGCGGTGCAGAGCCTCCTGTCGCGCGAGAGCCGGCACGACATCCGCCGCCTGGACCTGAGCTTCTCGAGGGAAG

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 63.40% 36.00% 0.13% 0.53% NA
All Indica  2759 39.70% 59.40% 0.14% 0.76% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 84.80% 14.90% 0.37% 0.00% NA
Indica I  595 4.90% 93.90% 0.00% 1.18% NA
Indica II  465 85.60% 13.80% 0.00% 0.65% NA
Indica III  913 37.00% 62.10% 0.33% 0.55% NA
Indica Intermediate  786 42.10% 57.00% 0.13% 0.76% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 73.30% 21.10% 1.11% 4.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0424200736 G -> DEL LOC_Os04g40780.1 N frameshift_variant Average:79.471; most accessible tissue: Zhenshan97 panicle, score: 96.13 N N N N
vg0424200736 G -> A LOC_Os04g40780.1 synonymous_variant ; p.Ala65Ala; LOW synonymous_codon Average:79.471; most accessible tissue: Zhenshan97 panicle, score: 96.13 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)
vg0424200736 G A -0.02 -0.01 -0.01 0.0 -0.01 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0424200736 NA 2.12E-14 Grain_length Ind_All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0424200736 NA 1.34E-08 mr1050 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
vg0424200736 NA 3.51E-07 mr1050 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
vg0424200736 NA 9.06E-06 mr1170 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
vg0424200736 NA 2.89E-06 mr1324 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
vg0424200736 NA 1.12E-06 mr1333 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
vg0424200736 NA 4.50E-08 mr1707 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
vg0424200736 NA 2.39E-08 mr1728 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
vg0424200736 NA 2.90E-09 mr1860 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
vg0424200736 NA 7.09E-06 mr1974 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
vg0424200736 NA 5.60E-06 mr1355_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
vg0424200736 NA 6.19E-06 mr1655_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
vg0424200736 NA 6.00E-12 mr1728_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
vg0424200736 NA 1.12E-08 mr1860_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
vg0424200736 NA 1.39E-07 mr1895_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
vg0424200736 NA 6.20E-07 mr1904_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
vg0424200736 NA 1.49E-06 mr1910_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
vg0424200736 NA 2.20E-06 mr1942_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