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Search for Variation information by Variation ID:

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

Detailed information for vg0431810267:

Variant ID: vg0431810267 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 31810267
Reference Allele: GAlternative Allele: C
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.85, C: 0.15, others allele: 0.00, population size: 82. )

Flanking Sequence (100 bp) in Reference Genome:


GGCGGCGACGACTGCGTCACGTTCAGGTGCTCCCTGACCGTCATCAGGGAGCCTCGCACCGAGGGCGTGGCCGCCGTCGCCGTGCCGCCGTCGGACATGC[G/C]
CCGGCACATGGCGAACATGCTGAGGGGCGGCGACGGCGCGGACGTGGTGGTGCTGGTGCGCGACCAGCCGTTCCGCGCCCACCGCTGCGTGCTCGCCGCG

Reverse complement sequence

CGCGGCGAGCACGCAGCGGTGGGCGCGGAACGGCTGGTCGCGCACCAGCACCACCACGTCCGCGCCGTCGCCGCCCCTCAGCATGTTCGCCATGTGCCGG[C/G]
GCATGTCCGACGGCGGCACGGCGACGGCGGCCACGCCCTCGGTGCGAGGCTCCCTGATGACGGTCAGGGAGCACCTGAACGTGACGCAGTCGTCGCCGCC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 71.40% 28.10% 0.49% 0.00% NA
All Indica  2759 82.00% 17.90% 0.14% 0.00% NA
All Japonica  1512 55.30% 43.50% 1.26% 0.00% NA
Aus  269 65.80% 34.20% 0.00% 0.00% NA
Indica I  595 87.70% 12.30% 0.00% 0.00% NA
Indica II  465 65.20% 34.80% 0.00% 0.00% NA
Indica III  913 90.10% 9.90% 0.00% 0.00% NA
Indica Intermediate  786 78.10% 21.40% 0.51% 0.00% NA
Temperate Japonica  767 80.20% 17.50% 2.35% 0.00% NA
Tropical Japonica  504 25.80% 74.20% 0.00% 0.00% NA
Japonica Intermediate  241 37.80% 61.80% 0.41% 0.00% NA
VI/Aromatic  96 37.50% 62.50% 0.00% 0.00% NA
Intermediate  90 72.20% 27.80% 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
vg0431810267 G -> C LOC_Os04g53400.1 missense_variant ; p.Arg187Pro; MODERATE nonsynonymous_codon ; R187P Average:85.019; most accessible tissue: Zhenshan97 panicle, score: 91.03 unknown unknown TOLERATED 0.08

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)
vg0431810267 G C 0.0 0.0 0.0 0.0 0.01 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0431810267 NA 4.39E-10 Heading_date Jap_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
vg0431810267 NA 6.91E-12 Spikelet_length Jap_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
vg0431810267 NA 4.31E-06 mr1588 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
vg0431810267 2.99E-06 NA mr1642 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
vg0431810267 NA 2.46E-07 mr1902 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
vg0431810267 NA 2.47E-06 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
vg0431810267 9.32E-06 9.28E-06 mr1197_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
vg0431810267 NA 5.04E-08 mr1229_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
vg0431810267 NA 3.33E-08 mr1521_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
vg0431810267 NA 6.39E-07 mr1671_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
vg0431810267 NA 8.94E-06 mr1865_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
vg0431810267 NA 3.69E-09 mr1880_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