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Detailed information for vg1222577056:

Variant ID: vg1222577056 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 22577056
Reference Allele: CAlternative Allele: G
Primary Allele: CSecondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.89, G: 0.10, others allele: 0.00, population size: 245. )

Flanking Sequence (100 bp) in Reference Genome:


CATTCCAAAATAAAGAAAATTGGATAGTAGTAGATTGGATCAGTGCATTAATTGCTTTGTGGGTCCTAGCCTCATCATAGCATCTCCAGAGCAACTTGAA[C/G]
ACAAAAAATGGGACCAAAGGGATGGCCGGAAGGCTATCGAAGTATCAATTCTTGGCATGTCCTTCTAAGAACCGCGATGTGGATTAGTGATGCAATTAAT

Reverse complement sequence

ATTAATTGCATCACTAATCCACATCGCGGTTCTTAGAAGGACATGCCAAGAATTGATACTTCGATAGCCTTCCGGCCATCCCTTTGGTCCCATTTTTTGT[G/C]
TTCAAGTTGCTCTGGAGATGCTATGATGAGGCTAGGACCCACAAAGCAATTAATGCACTGATCCAATCTACTACTATCCAATTTTCTTTATTTTGGAATG

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 79.30% 10.00% 5.33% 5.37% NA
All Indica  2759 65.30% 16.70% 8.92% 9.10% NA
All Japonica  1512 99.50% 0.40% 0.00% 0.07% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 71.60% 8.10% 12.94% 7.39% NA
Indica II  465 36.60% 38.30% 8.60% 16.56% NA
Indica III  913 82.80% 10.20% 3.07% 3.94% NA
Indica Intermediate  786 57.30% 17.90% 12.85% 11.96% NA
Temperate Japonica  767 99.30% 0.70% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.00% 0.00% 0.20% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 95.80% 1.00% 2.08% 1.04% NA
Intermediate  90 88.90% 5.60% 4.44% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1222577056 C -> DEL N N silent_mutation Average:81.228; most accessible tissue: Zhenshan97 panicle, score: 95.016 N N N N
vg1222577056 C -> G LOC_Os12g36820.1 upstream_gene_variant ; 1139.0bp to feature; MODIFIER silent_mutation Average:81.228; most accessible tissue: Zhenshan97 panicle, score: 95.016 N N N N
vg1222577056 C -> G LOC_Os12g36830.1 upstream_gene_variant ; 3722.0bp to feature; MODIFIER silent_mutation Average:81.228; most accessible tissue: Zhenshan97 panicle, score: 95.016 N N N N
vg1222577056 C -> G LOC_Os12g36810.1 downstream_gene_variant ; 767.0bp to feature; MODIFIER silent_mutation Average:81.228; most accessible tissue: Zhenshan97 panicle, score: 95.016 N N N N
vg1222577056 C -> G LOC_Os12g36810-LOC_Os12g36820 intergenic_region ; MODIFIER silent_mutation Average:81.228; most accessible tissue: Zhenshan97 panicle, score: 95.016 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)
vg1222577056 C G 0.05 0.1 0.09 0.09 0.08 0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1222577056 NA 1.49E-08 mr1011 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
vg1222577056 NA 2.53E-06 mr1011 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
vg1222577056 NA 2.03E-15 mr1013 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
vg1222577056 NA 1.08E-08 mr1013 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
vg1222577056 NA 4.79E-06 mr1015 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
vg1222577056 NA 2.28E-06 mr1021 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
vg1222577056 NA 3.95E-06 mr1030 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
vg1222577056 NA 1.23E-15 mr1031 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
vg1222577056 NA 2.08E-08 mr1031 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
vg1222577056 NA 8.71E-14 mr1034 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
vg1222577056 NA 3.24E-06 mr1034 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
vg1222577056 NA 1.76E-15 mr1056 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
vg1222577056 NA 5.38E-08 mr1056 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
vg1222577056 NA 2.52E-07 mr1660 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
vg1222577056 NA 4.95E-07 mr1739 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
vg1222577056 NA 2.98E-08 mr1739 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
vg1222577056 NA 6.81E-06 mr1965 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
vg1222577056 1.84E-06 1.84E-06 mr1966 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
vg1222577056 NA 1.62E-09 mr1174_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
vg1222577056 NA 4.31E-06 mr1268_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
vg1222577056 NA 2.08E-06 mr1389_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
vg1222577056 NA 5.60E-09 mr1739_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