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Detailed information for vg1121998197:

Variant ID: vg1121998197 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 21998197
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.64, A: 0.37, others allele: 0.00, population size: 86. )

Flanking Sequence (100 bp) in Reference Genome:


GGAGCTCAGCGGGTGGGCGGATGAGTGCGACGATGGCTAGCGGCGAGAAGGAGTGGCGCAAGATTGCGAGCAGGCGGACAGACAGAGGAGGAGCACGGAT[G/A]
GGCGAGCAGGGGTGCAGTTGGAGGAGCACGACGATGGCCAAGCAGGCGGAGGAGCGCGACGGCTGTCGCGCGGGCGAAGGAGCAAGCTGGCGGCGAGTAG

Reverse complement sequence

CTACTCGCCGCCAGCTTGCTCCTTCGCCCGCGCGACAGCCGTCGCGCTCCTCCGCCTGCTTGGCCATCGTCGTGCTCCTCCAACTGCACCCCTGCTCGCC[C/T]
ATCCGTGCTCCTCCTCTGTCTGTCCGCCTGCTCGCAATCTTGCGCCACTCCTTCTCGCCGCTAGCCATCGTCGCACTCATCCGCCCACCCGCTGAGCTCC

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 50.80% 38.20% 2.12% 8.89% NA
All Indica  2759 66.50% 22.10% 1.88% 9.46% NA
All Japonica  1512 26.70% 68.50% 1.39% 3.37% NA
Aus  269 13.40% 47.20% 8.92% 30.48% NA
Indica I  595 46.20% 24.00% 6.55% 23.19% NA
Indica II  465 66.50% 32.00% 0.65% 0.86% NA
Indica III  913 78.60% 13.40% 0.33% 7.67% NA
Indica Intermediate  786 67.90% 24.90% 0.89% 6.23% NA
Temperate Japonica  767 15.00% 82.50% 0.39% 2.09% NA
Tropical Japonica  504 41.70% 49.40% 3.37% 5.56% NA
Japonica Intermediate  241 32.80% 63.90% 0.41% 2.90% NA
VI/Aromatic  96 76.00% 3.10% 1.04% 19.79% NA
Intermediate  90 57.80% 32.20% 2.22% 7.78% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1121998197 G -> A LOC_Os11g37240.1 missense_variant ; p.Met23Ile; MODERATE nonsynonymous_codon ; M23I Average:75.875; most accessible tissue: Zhenshan97 young leaf, score: 89.875 unknown unknown TOLERATED 0.67
vg1121998197 G -> DEL LOC_Os11g37240.1 N frameshift_variant Average:75.875; most accessible tissue: Zhenshan97 young leaf, score: 89.875 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)
vg1121998197 G A 0.0 0.0 0.0 0.0 0.01 0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1121998197 NA 2.25E-12 Heading_date 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
vg1121998197 NA 1.70E-06 mr1242_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
vg1121998197 5.62E-06 6.93E-08 mr1545_2 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
vg1121998197 NA 9.10E-06 mr1545_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
vg1121998197 NA 4.32E-06 mr1555_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
vg1121998197 NA 3.56E-06 mr1729_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
vg1121998197 NA 2.45E-07 mr1788_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
vg1121998197 NA 1.57E-06 mr1800_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