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Detailed information for vg0303778438:

Variant ID: vg0303778438 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 3778438
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 232. )

Flanking Sequence (100 bp) in Reference Genome:


CAACTTTTTTTCCCTGGACCCTGACGACGAGTCGACGACGACCAAAGCTCAAGTAGTCTCCTTACCGTTTTTGATGCGGTTACCACACCCCCACGGTAAG[G/T]
TGGTTACCACAGTAACCGCGTGATTACCACGAGACATACCGTAGTTTCAAAAATTGAAAAGGTTACCGTGTATAGTAACCGTGTGGTGACCGTGCGGTTT

Reverse complement sequence

AAACCGCACGGTCACCACACGGTTACTATACACGGTAACCTTTTCAATTTTTGAAACTACGGTATGTCTCGTGGTAATCACGCGGTTACTGTGGTAACCA[C/A]
CTTACCGTGGGGGTGTGGTAACCGCATCAAAAACGGTAAGGAGACTACTTGAGCTTTGGTCGTCGTCGACTCGTCGTCAGGGTCCAGGGAAAAAAAGTTG

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 92.60% 7.40% 0.02% 0.00% NA
All Indica  2759 99.90% 0.10% 0.00% 0.00% NA
All Japonica  1512 80.20% 19.70% 0.07% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.60% 0.40% 0.00% 0.00% NA
Temperate Japonica  767 80.40% 19.60% 0.00% 0.00% NA
Tropical Japonica  504 92.90% 7.10% 0.00% 0.00% NA
Japonica Intermediate  241 53.10% 46.50% 0.41% 0.00% NA
VI/Aromatic  96 57.30% 42.70% 0.00% 0.00% NA
Intermediate  90 93.30% 6.70% 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
vg0303778438 G -> T LOC_Os03g07440.1 upstream_gene_variant ; 817.0bp to feature; MODIFIER silent_mutation Average:92.215; most accessible tissue: Minghui63 flower, score: 98.03 N N N N
vg0303778438 G -> T LOC_Os03g07440-LOC_Os03g07450 intergenic_region ; MODIFIER silent_mutation Average:92.215; most accessible tissue: Minghui63 flower, score: 98.03 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)
vg0303778438 G T -0.1 -0.22 -0.18 -0.11 -0.11 -0.12

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0303778438 NA 6.65E-08 mr1004_2 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
vg0303778438 7.84E-06 7.84E-06 mr1004_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
vg0303778438 NA 9.70E-08 mr1010_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
vg0303778438 NA 3.34E-08 mr1051_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
vg0303778438 NA 6.43E-07 mr1183_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