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Detailed information for vg0212876512:

Variant ID: vg0212876512 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 12876512
Reference Allele: CAlternative Allele: A,T
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 318. )

Flanking Sequence (100 bp) in Reference Genome:


CTCAATTTTGGACGAGGGAGTTCAAGTGCAGGAAATTTACGGTGGTCGAGCTAGGGTTTTGCAGAGTTCGTGCCCAACAATGGTGGATGGCCGGGTATCT[C/A,T]
TGGTTAGATGGTAGAAAAGATCGATATGAACTCTCTTTCTCCCATAGTGAGGGTTGAATTTAGGTTAGAGCGGTGGTGGAGCTTGGGCAACGGGAAAACT

Reverse complement sequence

AGTTTTCCCGTTGCCCAAGCTCCACCACCGCTCTAACCTAAATTCAACCCTCACTATGGGAGAAAGAGAGTTCATATCGATCTTTTCTACCATCTAACCA[G/T,A]
AGATACCCGGCCATCCACCATTGTTGGGCACGAACTCTGCAAAACCCTAGCTCGACCACCGTAAATTTCCTGCACTTGAACTCCCTCGTCCAAAATTGAG

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 87.30% 12.30% 0.28% 0.00% T: 0.13%
All Indica  2759 99.60% 0.40% 0.00% 0.00% NA
All Japonica  1512 62.50% 36.60% 0.86% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 98.90% 1.10% 0.00% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 99.50% 0.50% 0.00% 0.00% NA
Temperate Japonica  767 93.70% 6.00% 0.26% 0.00% NA
Tropical Japonica  504 11.90% 86.70% 1.39% 0.00% NA
Japonica Intermediate  241 68.90% 29.50% 1.66% 0.00% NA
VI/Aromatic  96 91.70% 2.10% 0.00% 0.00% T: 6.25%
Intermediate  90 83.30% 16.70% 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
vg0212876512 C -> A LOC_Os02g21660.1 downstream_gene_variant ; 4040.0bp to feature; MODIFIER silent_mutation Average:79.872; most accessible tissue: Zhenshan97 panicle, score: 91.693 N N N N
vg0212876512 C -> A LOC_Os02g21670.1 downstream_gene_variant ; 380.0bp to feature; MODIFIER silent_mutation Average:79.872; most accessible tissue: Zhenshan97 panicle, score: 91.693 N N N N
vg0212876512 C -> A LOC_Os02g21660.2 downstream_gene_variant ; 4041.0bp to feature; MODIFIER silent_mutation Average:79.872; most accessible tissue: Zhenshan97 panicle, score: 91.693 N N N N
vg0212876512 C -> A LOC_Os02g21660.3 downstream_gene_variant ; 4041.0bp to feature; MODIFIER silent_mutation Average:79.872; most accessible tissue: Zhenshan97 panicle, score: 91.693 N N N N
vg0212876512 C -> A LOC_Os02g21660-LOC_Os02g21670 intergenic_region ; MODIFIER silent_mutation Average:79.872; most accessible tissue: Zhenshan97 panicle, score: 91.693 N N N N
vg0212876512 C -> T LOC_Os02g21660.1 downstream_gene_variant ; 4040.0bp to feature; MODIFIER silent_mutation Average:79.872; most accessible tissue: Zhenshan97 panicle, score: 91.693 N N N N
vg0212876512 C -> T LOC_Os02g21670.1 downstream_gene_variant ; 380.0bp to feature; MODIFIER silent_mutation Average:79.872; most accessible tissue: Zhenshan97 panicle, score: 91.693 N N N N
vg0212876512 C -> T LOC_Os02g21660.2 downstream_gene_variant ; 4041.0bp to feature; MODIFIER silent_mutation Average:79.872; most accessible tissue: Zhenshan97 panicle, score: 91.693 N N N N
vg0212876512 C -> T LOC_Os02g21660.3 downstream_gene_variant ; 4041.0bp to feature; MODIFIER silent_mutation Average:79.872; most accessible tissue: Zhenshan97 panicle, score: 91.693 N N N N
vg0212876512 C -> T LOC_Os02g21660-LOC_Os02g21670 intergenic_region ; MODIFIER silent_mutation Average:79.872; 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)
vg0212876512 C A -0.02 -0.02 -0.02 -0.01 -0.03 -0.03
vg0212876512 C T -0.01 -0.02 -0.02 -0.02 0.0 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0212876512 NA 4.06E-22 mr1301 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
vg0212876512 NA 8.53E-15 mr1301 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
vg0212876512 5.29E-06 NA mr1364 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
vg0212876512 NA 1.54E-08 mr1364 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
vg0212876512 NA 2.87E-06 mr1398 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
vg0212876512 1.93E-06 NA mr1443 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
vg0212876512 NA 3.82E-09 mr1443 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
vg0212876512 NA 7.23E-14 mr1449 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
vg0212876512 NA 1.00E-09 mr1533 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
vg0212876512 NA 2.00E-07 mr1551 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
vg0212876512 NA 8.18E-13 mr1578 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
vg0212876512 NA 1.34E-08 mr1648 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
vg0212876512 NA 4.33E-07 mr1668 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
vg0212876512 NA 4.25E-34 mr1699 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
vg0212876512 NA 2.08E-18 mr1715 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
vg0212876512 NA 4.10E-13 mr1769 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
vg0212876512 NA 3.37E-06 mr1942 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
vg0212876512 NA 2.44E-09 mr1980 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
vg0212876512 NA 3.54E-08 mr1993 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
vg0212876512 NA 1.34E-22 mr1301_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
vg0212876512 NA 2.88E-16 mr1301_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
vg0212876512 NA 1.98E-10 mr1354_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
vg0212876512 NA 9.92E-10 mr1379_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
vg0212876512 NA 4.74E-11 mr1398_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
vg0212876512 NA 6.62E-07 mr1398_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
vg0212876512 NA 3.14E-07 mr1551_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
vg0212876512 NA 3.38E-21 mr1593_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
vg0212876512 NA 8.04E-07 mr1696_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
vg0212876512 NA 2.30E-37 mr1699_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
vg0212876512 NA 8.60E-17 mr1699_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
vg0212876512 NA 1.71E-10 mr1705_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
vg0212876512 NA 3.71E-10 mr1761_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
vg0212876512 NA 4.13E-07 mr1819_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
vg0212876512 NA 3.13E-09 mr1916_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
vg0212876512 NA 2.96E-11 mr1993_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
vg0212876512 NA 8.80E-13 mr1993_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