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Detailed information for vg1003401204:

Variant ID: vg1003401204 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 3401204
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.96, A: 0.04, others allele: 0.00, population size: 109. )

Flanking Sequence (100 bp) in Reference Genome:


CTGATGCATCGAGTCAACTCCATCGAAATCATCACGAAAATCATCCAAACACAATAACAAAAATCGATTCCCCTACCTTCCCATCGTTGATCTAGCTGCC[C/A]
CCACCATCATGGCAGCCAGCGGCGGAGAGGAGGCGCCTTCCCTCTTGCTGGCACTGCCACTGCCTTCCCTCTCGCCGGATCTAGTGGAGGGGAGCCCAAC

Reverse complement sequence

GTTGGGCTCCCCTCCACTAGATCCGGCGAGAGGGAAGGCAGTGGCAGTGCCAGCAAGAGGGAAGGCGCCTCCTCTCCGCCGCTGGCTGCCATGATGGTGG[G/T]
GGCAGCTAGATCAACGATGGGAAGGTAGGGGAATCGATTTTTGTTATTGTGTTTGGATGATTTTCGTGATGATTTCGATGGAGTTGACTCGATGCATCAG

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 59.40% 40.20% 0.21% 0.23% NA
All Indica  2759 43.30% 56.00% 0.25% 0.40% NA
All Japonica  1512 98.30% 1.70% 0.07% 0.00% NA
Aus  269 7.10% 92.90% 0.00% 0.00% NA
Indica I  595 46.20% 53.10% 0.34% 0.34% NA
Indica II  465 25.80% 72.90% 0.43% 0.86% NA
Indica III  913 58.80% 40.60% 0.22% 0.33% NA
Indica Intermediate  786 33.60% 66.00% 0.13% 0.25% NA
Temperate Japonica  767 99.60% 0.40% 0.00% 0.00% NA
Tropical Japonica  504 96.20% 3.80% 0.00% 0.00% NA
Japonica Intermediate  241 98.30% 1.20% 0.41% 0.00% NA
VI/Aromatic  96 58.30% 41.70% 0.00% 0.00% NA
Intermediate  90 55.60% 42.20% 2.22% 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
vg1003401204 C -> A LOC_Os10g06600.1 upstream_gene_variant ; 2968.0bp to feature; MODIFIER silent_mutation Average:75.545; most accessible tissue: Minghui63 panicle, score: 87.238 N N N N
vg1003401204 C -> A LOC_Os10g06600-LOC_Os10g06610 intergenic_region ; MODIFIER silent_mutation Average:75.545; most accessible tissue: Minghui63 panicle, score: 87.238 N N N N
vg1003401204 C -> DEL N N silent_mutation Average:75.545; most accessible tissue: Minghui63 panicle, score: 87.238 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)
vg1003401204 C A -0.04 -0.02 -0.02 -0.03 -0.04 -0.04

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1003401204 NA 1.26E-06 mr1291 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
vg1003401204 4.88E-12 NA mr1538 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
vg1003401204 2.26E-12 1.84E-14 mr1538 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
vg1003401204 1.57E-20 8.28E-14 mr1547 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
vg1003401204 7.86E-20 4.68E-26 mr1547 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
vg1003401204 7.42E-35 1.93E-46 mr1709 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
vg1003401204 1.32E-36 4.75E-63 mr1709 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
vg1003401204 NA 5.39E-07 mr1129_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
vg1003401204 NA 9.44E-07 mr1251_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
vg1003401204 NA 1.12E-06 mr1435_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
vg1003401204 1.17E-11 NA mr1538_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
vg1003401204 1.62E-15 1.91E-20 mr1538_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
vg1003401204 3.14E-19 1.63E-18 mr1547_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
vg1003401204 1.00E-21 5.48E-30 mr1547_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
vg1003401204 5.42E-50 1.60E-71 mr1709_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
vg1003401204 1.42E-44 6.04E-101 mr1709_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