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Detailed information for vg1203610578:

Variant ID: vg1203610578 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 3610578
Reference Allele: CAlternative Allele: A
Primary Allele: ASecondary Allele: C

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 277. )

Flanking Sequence (100 bp) in Reference Genome:


ACCACTTTCGTCCGATAAAGGGGACTGTTCCATTTGTATGTCCAAGTGTCTTCTGAGCTATTAAGGGAAACCCAATTGAGATTGGACTGGATTGTTTGCC[C/A]
CTCCTGCATTGCTTGGGTAGATAAAGGTGTGTGTAGCAGGTTTTCTAAATTTTGTTCTGATAGAAAACCAAAGACTGAGATATCTTCTTTTGCAACAAAG

Reverse complement sequence

CTTTGTTGCAAAAGAAGATATCTCAGTCTTTGGTTTTCTATCAGAACAAAATTTAGAAAACCTGCTACACACACCTTTATCTACCCAAGCAATGCAGGAG[G/T]
GGCAAACAATCCAGTCCAATCTCAATTGGGTTTCCCTTAATAGCTCAGAAGACACTTGGACATACAAATGGAACAGTCCCCTTTATCGGACGAAAGTGGT

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 80.50% 18.40% 1.08% 0.00% NA
All Indica  2759 98.00% 1.50% 0.47% 0.00% NA
All Japonica  1512 46.60% 51.10% 2.31% 0.00% NA
Aus  269 88.10% 11.20% 0.74% 0.00% NA
Indica I  595 99.50% 0.50% 0.00% 0.00% NA
Indica II  465 98.70% 1.10% 0.22% 0.00% NA
Indica III  913 97.90% 0.90% 1.20% 0.00% NA
Indica Intermediate  786 96.60% 3.30% 0.13% 0.00% NA
Temperate Japonica  767 32.10% 64.30% 3.65% 0.00% NA
Tropical Japonica  504 73.20% 26.60% 0.20% 0.00% NA
Japonica Intermediate  241 37.30% 60.20% 2.49% 0.00% NA
VI/Aromatic  96 95.80% 4.20% 0.00% 0.00% NA
Intermediate  90 75.60% 23.30% 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
vg1203610578 C -> A LOC_Os12g07340.1 upstream_gene_variant ; 780.0bp to feature; MODIFIER silent_mutation Average:61.023; most accessible tissue: Zhenshan97 flower, score: 84.783 N N N N
vg1203610578 C -> A LOC_Os12g07310-LOC_Os12g07340 intergenic_region ; MODIFIER silent_mutation Average:61.023; most accessible tissue: Zhenshan97 flower, score: 84.783 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)
vg1203610578 C A -0.05 -0.03 -0.03 -0.04 -0.1 -0.07

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1203610578 NA 4.83E-07 mr1092 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
vg1203610578 NA 1.33E-07 mr1097 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
vg1203610578 NA 2.13E-06 mr1149 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
vg1203610578 NA 3.38E-06 mr1154 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
vg1203610578 NA 1.14E-06 mr1163 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
vg1203610578 NA 1.55E-06 mr1748 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
vg1203610578 NA 1.09E-09 mr1011_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
vg1203610578 NA 4.06E-06 mr1011_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
vg1203610578 NA 1.20E-06 mr1097_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
vg1203610578 NA 7.17E-06 mr1154_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
vg1203610578 NA 1.85E-06 mr1330_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
vg1203610578 NA 1.46E-13 mr1709_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