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Detailed information for vg0401005726:

Variant ID: vg0401005726 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 1005726
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.81, A: 0.18, others allele: 0.00, population size: 99. )

Flanking Sequence (100 bp) in Reference Genome:


CGTGGAGTAACCTGCACTCACCATCGCGGAGAAGTCCGTCCGCACACCGCCCACGCGTGGATCTGGCCATCCCAAGCTCTGGCCAAATCCGGTGGCCACT[G/A]
CGCTGGGCCAGGGAGTGGAAGAGGTAGCCGCCACCACCGTCATGCCGCATAGGGGAGAGGAAGTTGTGTTCACTGCCATTGTGCACAGGGGATAGCCGCC

Reverse complement sequence

GGCGGCTATCCCCTGTGCACAATGGCAGTGAACACAACTTCCTCTCCCCTATGCGGCATGACGGTGGTGGCGGCTACCTCTTCCACTCCCTGGCCCAGCG[C/T]
AGTGGCCACCGGATTTGGCCAGAGCTTGGGATGGCCAGATCCACGCGTGGGCGGTGTGCGGACGGACTTCTCCGCGATGGTGAGTGCAGGTTACTCCACG

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 82.30% 17.60% 0.11% 0.00% NA
All Indica  2759 78.60% 21.20% 0.18% 0.00% NA
All Japonica  1512 89.70% 10.30% 0.00% 0.00% NA
Aus  269 99.30% 0.70% 0.00% 0.00% NA
Indica I  595 96.60% 3.40% 0.00% 0.00% NA
Indica II  465 70.80% 29.00% 0.22% 0.00% NA
Indica III  913 67.90% 31.90% 0.22% 0.00% NA
Indica Intermediate  786 82.10% 17.70% 0.25% 0.00% NA
Temperate Japonica  767 91.50% 8.50% 0.00% 0.00% NA
Tropical Japonica  504 91.50% 8.50% 0.00% 0.00% NA
Japonica Intermediate  241 80.50% 19.50% 0.00% 0.00% NA
VI/Aromatic  96 21.90% 78.10% 0.00% 0.00% NA
Intermediate  90 85.60% 14.40% 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
vg0401005726 G -> A LOC_Os04g02660.1 missense_variant ; p.Ala27Val; MODERATE nonsynonymous_codon ; A27V Average:75.351; most accessible tissue: Minghui63 young leaf, score: 85.826 unknown unknown DELETERIOUS 0.00

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)
vg0401005726 G A -0.16 -0.09 -0.08 -0.12 -0.15 -0.16

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0401005726 4.40E-07 4.40E-07 mr1343 Jap_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
vg0401005726 NA 4.73E-06 mr1354 Jap_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
vg0401005726 7.29E-07 8.72E-08 mr1829 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
vg0401005726 1.46E-06 3.30E-09 mr1829 Jap_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
vg0401005726 8.09E-07 NA mr1842 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
vg0401005726 7.40E-06 7.40E-06 mr1842 Jap_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
vg0401005726 NA 2.49E-08 mr1354_2 Jap_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
vg0401005726 3.73E-06 1.55E-09 mr1829_2 Jap_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
vg0401005726 NA 8.26E-06 mr1842_2 Jap_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
vg0401005726 NA 1.10E-07 mr1902_2 Jap_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