Search for Variation information by Variation ID:

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

Detailed information for vg1002434615:

Variant ID: vg1002434615 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 2434615
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.96, G: 0.05, others allele: 0.00, population size: 195. )

Flanking Sequence (100 bp) in Reference Genome:


CAGGTAGCCATTGTGAACCGGCACCAATGGCCTATCCAGTGGTAGTGACAGACACACAGTAACACATACTCCCTCCGTCCCATATTATAACAATGAATTT[A/G]
CACATGCTTCCTGTTTAGATTAGTTGTACTATAAAGTGCATCCGGTCCTAGGTTGTTATATTATGAGACGTAGGGAGTATATACCTACACACACAAATAT

Reverse complement sequence

ATATTTGTGTGTGTAGGTATATACTCCCTACGTCTCATAATATAACAACCTAGGACCGGATGCACTTTATAGTACAACTAATCTAAACAGGAAGCATGTG[T/C]
AAATTCATTGTTATAATATGGGACGGAGGGAGTATGTGTTACTGTGTGTCTGTCACTACCACTGGATAGGCCATTGGTGCCGGTTCACAATGGCTACCTG

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 57.20% 36.00% 0.21% 6.62% NA
All Indica  2759 79.40% 13.10% 0.14% 7.32% NA
All Japonica  1512 30.50% 69.00% 0.20% 0.26% NA
Aus  269 0.40% 90.00% 0.00% 9.67% NA
Indica I  595 69.70% 5.50% 0.17% 24.54% NA
Indica II  465 89.70% 8.80% 0.00% 1.51% NA
Indica III  913 80.90% 17.90% 0.22% 0.99% NA
Indica Intermediate  786 79.00% 15.80% 0.13% 5.09% NA
Temperate Japonica  767 39.90% 59.80% 0.13% 0.13% NA
Tropical Japonica  504 7.30% 92.30% 0.40% 0.00% NA
Japonica Intermediate  241 49.00% 49.80% 0.00% 1.24% NA
VI/Aromatic  96 2.10% 20.80% 2.08% 75.00% NA
Intermediate  90 50.00% 38.90% 1.11% 10.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1002434615 A -> G LOC_Os10g05000.1 upstream_gene_variant ; 4214.0bp to feature; MODIFIER silent_mutation Average:76.82; most accessible tissue: Zhenshan97 panicle, score: 91.693 N N N N
vg1002434615 A -> G LOC_Os10g04990.1 downstream_gene_variant ; 1964.0bp to feature; MODIFIER silent_mutation Average:76.82; most accessible tissue: Zhenshan97 panicle, score: 91.693 N N N N
vg1002434615 A -> G LOC_Os10g04990-LOC_Os10g05000 intergenic_region ; MODIFIER silent_mutation Average:76.82; most accessible tissue: Zhenshan97 panicle, score: 91.693 N N N N
vg1002434615 A -> DEL N N silent_mutation Average:76.82; most accessible tissue: Zhenshan97 panicle, score: 91.693 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)
vg1002434615 A G -0.03 -0.03 -0.01 -0.09 -0.03 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1002434615 NA 1.48E-06 mr1029 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
vg1002434615 NA 8.98E-06 mr1189 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
vg1002434615 NA 9.40E-08 mr1610 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
vg1002434615 NA 9.10E-06 mr1625 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
vg1002434615 NA 5.07E-06 mr1782 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
vg1002434615 NA 2.49E-06 mr1818 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
vg1002434615 NA 1.20E-16 mr1825 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
vg1002434615 NA 6.95E-06 mr1123_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
vg1002434615 2.23E-06 1.97E-06 mr1242_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
vg1002434615 NA 7.29E-06 mr1818_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
vg1002434615 NA 7.09E-06 mr1927_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