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Detailed information for vg1121219893:

Variant ID: vg1121219893 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 21219893
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TGTGCTCAAATCTCGCCCGAAATTTTAGGTTTTTTACAATTTTTTTGTGAATTTGGTCAAATTTTATTTAAATTCAGTCAAATTTTCAAATAATTTCGGC[C/T]
AGAAATTTCCAAAATTTTGGTCACCCCCAGCATAAAATCCAATTTCGAAATTGAAAACCCTGTCTCGCGGTCGCTAGTTTCGGCGTTGGTCAGTCCACCG

Reverse complement sequence

CGGTGGACTGACCAACGCCGAAACTAGCGACCGCGAGACAGGGTTTTCAATTTCGAAATTGGATTTTATGCTGGGGGTGACCAAAATTTTGGAAATTTCT[G/A]
GCCGAAATTATTTGAAAATTTGACTGAATTTAAATAAAATTTGACCAAATTCACAAAAAAATTGTAAAAAACCTAAAATTTCGGGCGAGATTTGAGCACA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 74.20% 20.20% 2.35% 3.24% NA
All Indica  2759 86.00% 12.50% 0.33% 1.20% NA
All Japonica  1512 51.90% 35.60% 6.42% 6.15% NA
Aus  269 81.00% 10.40% 0.74% 7.81% NA
Indica I  595 98.20% 1.70% 0.17% 0.00% NA
Indica II  465 96.10% 3.40% 0.00% 0.43% NA
Indica III  913 73.90% 23.10% 0.44% 2.52% NA
Indica Intermediate  786 84.90% 13.60% 0.51% 1.02% NA
Temperate Japonica  767 84.20% 11.70% 2.87% 1.17% NA
Tropical Japonica  504 14.50% 64.90% 9.52% 11.11% NA
Japonica Intermediate  241 27.00% 50.20% 11.20% 11.62% NA
VI/Aromatic  96 66.70% 27.10% 2.08% 4.17% NA
Intermediate  90 73.30% 23.30% 1.11% 2.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1121219893 C -> T LOC_Os11g36090.1 upstream_gene_variant ; 3580.0bp to feature; MODIFIER silent_mutation Average:68.925; most accessible tissue: Zhenshan97 flag leaf, score: 91.687 N N N N
vg1121219893 C -> T LOC_Os11g36100.1 upstream_gene_variant ; 4909.0bp to feature; MODIFIER silent_mutation Average:68.925; most accessible tissue: Zhenshan97 flag leaf, score: 91.687 N N N N
vg1121219893 C -> T LOC_Os11g36090-LOC_Os11g36100 intergenic_region ; MODIFIER silent_mutation Average:68.925; most accessible tissue: Zhenshan97 flag leaf, score: 91.687 N N N N
vg1121219893 C -> DEL N N silent_mutation Average:68.925; most accessible tissue: Zhenshan97 flag leaf, score: 91.687 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)
vg1121219893 C T 0.04 0.01 0.01 0.03 0.05 0.05

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1121219893 NA 7.82E-13 Heading_date Ind_All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg1121219893 NA 1.30E-06 mr1206 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
vg1121219893 NA 7.33E-06 mr1215 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
vg1121219893 1.41E-07 1.41E-07 mr1260 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
vg1121219893 NA 1.03E-08 mr1332 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
vg1121219893 NA 1.34E-12 mr1454 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
vg1121219893 NA 2.18E-08 mr1506 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
vg1121219893 NA 8.17E-06 mr1508 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
vg1121219893 NA 6.41E-12 mr1579 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
vg1121219893 NA 2.15E-20 mr1580 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
vg1121219893 NA 2.52E-07 mr1596 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
vg1121219893 NA 5.59E-08 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
vg1121219893 NA 5.75E-07 mr1729 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
vg1121219893 NA 3.73E-06 mr1729 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
vg1121219893 NA 5.88E-06 mr1763 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
vg1121219893 NA 1.55E-10 mr1775 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
vg1121219893 NA 7.60E-08 mr1779 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
vg1121219893 NA 5.27E-07 mr1824 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
vg1121219893 NA 4.43E-06 mr1870 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
vg1121219893 NA 5.45E-06 mr1182_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
vg1121219893 NA 5.10E-08 mr1244_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
vg1121219893 NA 1.83E-06 mr1580_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
vg1121219893 NA 1.11E-07 mr1668_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
vg1121219893 NA 1.50E-06 mr1870_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