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Detailed information for vg0431377813:

Variant ID: vg0431377813 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 31377813
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 245. )

Flanking Sequence (100 bp) in Reference Genome:


CTTGGTTTTATTTCATATGGCCGTACAGGCTAGTGATGTACTTAAGAGAAGTTGCTTTATATTTGGAAAAAAAAATCAAGGGTAGTAGCTAGTATGAAAT[G/A]
AATGAAGATATTTTGTAACCAAGATAAATGAATTGGCAAAATAATCTGTTCATTAATTATATAGTAGTACATAGTGGTCTTATCCTTCAACAGAAAATTG

Reverse complement sequence

CAATTTTCTGTTGAAGGATAAGACCACTATGTACTACTATATAATTAATGAACAGATTATTTTGCCAATTCATTTATCTTGGTTACAAAATATCTTCATT[C/T]
ATTTCATACTAGCTACTACCCTTGATTTTTTTTTCCAAATATAAAGCAACTTCTCTTAAGTACATCACTAGCCTGTACGGCCATATGAAATAAAACCAAG

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 91.10% 8.70% 0.19% 0.00% NA
All Indica  2759 93.60% 6.30% 0.07% 0.00% NA
All Japonica  1512 88.40% 11.20% 0.46% 0.00% NA
Aus  269 93.70% 6.30% 0.00% 0.00% NA
Indica I  595 97.30% 2.70% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 90.60% 9.30% 0.11% 0.00% NA
Indica Intermediate  786 90.70% 9.20% 0.13% 0.00% NA
Temperate Japonica  767 90.00% 9.10% 0.91% 0.00% NA
Tropical Japonica  504 95.80% 4.20% 0.00% 0.00% NA
Japonica Intermediate  241 67.60% 32.40% 0.00% 0.00% NA
VI/Aromatic  96 50.00% 50.00% 0.00% 0.00% NA
Intermediate  90 94.40% 5.60% 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
vg0431377813 G -> A LOC_Os04g52700.1 downstream_gene_variant ; 1452.0bp to feature; MODIFIER silent_mutation Average:70.252; most accessible tissue: Minghui63 young leaf, score: 93.523 N N N N
vg0431377813 G -> A LOC_Os04g52690-LOC_Os04g52700 intergenic_region ; MODIFIER silent_mutation Average:70.252; most accessible tissue: Minghui63 young leaf, score: 93.523 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)
vg0431377813 G A -0.01 -0.02 0.0 0.0 0.0 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0431377813 NA 2.11E-10 Heading_date 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
vg0431377813 NA 5.27E-07 mr1533 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
vg0431377813 NA 2.74E-08 mr1980 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
vg0431377813 NA 3.31E-06 mr1095_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
vg0431377813 NA 2.09E-12 mr1533_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
vg0431377813 NA 5.22E-10 mr1980_2 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