Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0432591580:

Variant ID: vg0432591580 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 32591580
Reference Allele: AAlternative Allele: C
Primary Allele: ASecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.95, A: 0.06, others allele: 0.00, population size: 259. )

Flanking Sequence (100 bp) in Reference Genome:


CAGGTTGCAGGTTATCAAGGCCTATTAAGCTCTAAAGACGCTGCTAATGCCCCCATCAATTACACTAAGACTCCCTAACAACCCGATGGCTACTGCACAT[A/C]
TCAACTCGTACTATAATTGCCTAGCTGCTAGGAATCGCGTTAATCAAACCAAACTTTAAAGGAAAATCAACGGTTTGATCTCGTCAGAGGTTAGACCATC

Reverse complement sequence

GATGGTCTAACCTCTGACGAGATCAAACCGTTGATTTTCCTTTAAAGTTTGGTTTGATTAACGCGATTCCTAGCAGCTAGGCAATTATAGTACGAGTTGA[T/G]
ATGTGCAGTAGCCATCGGGTTGTTAGGGAGTCTTAGTGTAATTGATGGGGGCATTAGCAGCGTCTTTAGAGCTTAATAGGCCTTGATAACCTGCAACCTG

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 67.50% 32.10% 0.11% 0.25% NA
All Indica  2759 77.10% 22.50% 0.04% 0.40% NA
All Japonica  1512 60.30% 39.60% 0.13% 0.07% NA
Aus  269 12.30% 87.40% 0.37% 0.00% NA
Indica I  595 91.30% 8.60% 0.00% 0.17% NA
Indica II  465 82.20% 17.20% 0.22% 0.43% NA
Indica III  913 62.20% 37.30% 0.00% 0.44% NA
Indica Intermediate  786 80.70% 18.80% 0.00% 0.51% NA
Temperate Japonica  767 64.90% 34.80% 0.26% 0.00% NA
Tropical Japonica  504 67.50% 32.30% 0.00% 0.20% NA
Japonica Intermediate  241 30.30% 69.70% 0.00% 0.00% NA
VI/Aromatic  96 61.50% 38.50% 0.00% 0.00% NA
Intermediate  90 66.70% 32.20% 1.11% 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
vg0432591580 A -> C LOC_Os04g54810.1 intron_variant ; MODIFIER silent_mutation Average:82.804; most accessible tissue: Minghui63 root, score: 90.372 N N N N
vg0432591580 A -> DEL N N silent_mutation Average:82.804; most accessible tissue: Minghui63 root, score: 90.372 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)
vg0432591580 A C 0.01 0.02 0.01 0.04 0.04 0.03

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0432591580 NA 3.32E-09 mr1403 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
vg0432591580 NA 8.97E-08 mr1403 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
vg0432591580 7.77E-07 1.02E-08 mr1800 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
vg0432591580 1.95E-06 3.87E-08 mr1800 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
vg0432591580 3.28E-06 NA mr1646_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
vg0432591580 NA 3.45E-07 mr1740_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
vg0432591580 1.08E-07 NA mr1741_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
vg0432591580 8.50E-06 NA mr1771_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
vg0432591580 2.28E-07 NA mr1784_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
vg0432591580 6.76E-06 NA mr1785_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
vg0432591580 NA 3.49E-06 mr1786_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
vg0432591580 8.01E-12 NA mr1800_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
vg0432591580 8.01E-12 1.57E-13 mr1800_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
vg0432591580 1.82E-06 NA mr1873_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