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Detailed information for vg0104231204:

Variant ID: vg0104231204 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 4231204
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 113. )

Flanking Sequence (100 bp) in Reference Genome:


AAACACTTGACGGCATATTGGACGGTATATGAAATATATAGTTAATGTACTCCCTATGACTTATAATATAACAATCTAGTATTGGATGGGGCACATCCTA[G/A]
TACTACGATATGTCTCATCCGATACTATGTTACTATATGAGACAGAAGGAGTAGATCATACTTTCTTCGTCCTAAAAAAACTTAACCTTATAATAATTGG

Reverse complement sequence

CCAATTATTATAAGGTTAAGTTTTTTTAGGACGAAGAAAGTATGATCTACTCCTTCTGTCTCATATAGTAACATAGTATCGGATGAGACATATCGTAGTA[C/T]
TAGGATGTGCCCCATCCAATACTAGATTGTTATATTATAAGTCATAGGGAGTACATTAACTATATATTTCATATACCGTCCAATATGCCGTCAAGTGTTT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 57.80% 42.10% 0.08% 0.00% NA
All Indica  2759 81.90% 17.90% 0.11% 0.00% NA
All Japonica  1512 12.40% 87.60% 0.00% 0.00% NA
Aus  269 74.00% 26.00% 0.00% 0.00% NA
Indica I  595 70.10% 29.90% 0.00% 0.00% NA
Indica II  465 95.10% 4.70% 0.22% 0.00% NA
Indica III  913 83.50% 16.30% 0.22% 0.00% NA
Indica Intermediate  786 81.40% 18.60% 0.00% 0.00% NA
Temperate Japonica  767 3.00% 97.00% 0.00% 0.00% NA
Tropical Japonica  504 30.40% 69.60% 0.00% 0.00% NA
Japonica Intermediate  241 4.60% 95.40% 0.00% 0.00% NA
VI/Aromatic  96 41.70% 58.30% 0.00% 0.00% NA
Intermediate  90 47.80% 51.10% 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
vg0104231204 G -> A LOC_Os01g08530.1 downstream_gene_variant ; 896.0bp to feature; MODIFIER silent_mutation Average:72.965; most accessible tissue: Callus, score: 94.125 N N N N
vg0104231204 G -> A LOC_Os01g08540.1 downstream_gene_variant ; 3310.0bp to feature; MODIFIER silent_mutation Average:72.965; most accessible tissue: Callus, score: 94.125 N N N N
vg0104231204 G -> A LOC_Os01g08520-LOC_Os01g08530 intergenic_region ; MODIFIER silent_mutation Average:72.965; most accessible tissue: Callus, score: 94.125 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)
vg0104231204 G A -0.02 -0.02 -0.03 -0.03 -0.03 -0.03

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0104231204 9.30E-06 NA mr1263 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
vg0104231204 NA 8.52E-10 mr1336 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
vg0104231204 9.30E-06 NA mr1451 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
vg0104231204 5.08E-06 5.08E-06 mr1076_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
vg0104231204 NA 1.68E-07 mr1205_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
vg0104231204 2.37E-07 1.50E-08 mr1498_2 Jap_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
vg0104231204 NA 4.44E-12 mr1641_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
vg0104231204 NA 1.35E-07 mr1681_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
vg0104231204 3.32E-06 3.32E-06 mr1925_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