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Detailed information for vg1128896330:

Variant ID: vg1128896330 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 28896330
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.97, G: 0.04, others allele: 0.00, population size: 254. )

Flanking Sequence (100 bp) in Reference Genome:


GCCAGAGGTGAGGATCACCATCGTTGACATCCCCCAGCCTGGGTTTCGTCCATTTCAGCGTATTGAGGCGGCAGGGCATTGCCTGAGCAGCTGTGCCAAT[G/A]
AGTTCCGCGTGCCATTCAGATTCCAAGCTGTTGTAGCAGCAAAGTGGGAGACGGTTGGTGCCGAGGACCTGCACATCGAGCCTGATGAGGTGCTTGTGGT

Reverse complement sequence

ACCACAAGCACCTCATCAGGCTCGATGTGCAGGTCCTCGGCACCAACCGTCTCCCACTTTGCTGCTACAACAGCTTGGAATCTGAATGGCACGCGGAACT[C/T]
ATTGGCACAGCTGCTCAGGCAATGCCCTGCCGCCTCAATACGCTGAAATGGACGAAACCCAGGCTGGGGGATGTCAACGATGGTGATCCTCACCTCTGGC

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 69.20% 30.70% 0.08% 0.02% NA
All Indica  2759 92.90% 7.00% 0.07% 0.04% NA
All Japonica  1512 21.00% 79.00% 0.07% 0.00% NA
Aus  269 98.90% 1.10% 0.00% 0.00% NA
Indica I  595 98.20% 1.70% 0.00% 0.17% NA
Indica II  465 95.30% 4.70% 0.00% 0.00% NA
Indica III  913 88.80% 11.20% 0.00% 0.00% NA
Indica Intermediate  786 92.20% 7.50% 0.25% 0.00% NA
Temperate Japonica  767 20.90% 79.00% 0.13% 0.00% NA
Tropical Japonica  504 21.80% 78.20% 0.00% 0.00% NA
Japonica Intermediate  241 19.50% 80.50% 0.00% 0.00% NA
VI/Aromatic  96 74.00% 26.00% 0.00% 0.00% NA
Intermediate  90 58.90% 40.00% 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
vg1128896330 G -> A LOC_Os11g47910.1 missense_variant ; p.Glu382Lys; MODERATE nonsynonymous_codon ; E382K Average:88.406; most accessible tissue: Zhenshan97 young leaf, score: 97.206 benign 0.223 TOLERATED 0.18
vg1128896330 G -> DEL LOC_Os11g47910.1 N frameshift_variant Average:88.406; most accessible tissue: Zhenshan97 young leaf, score: 97.206 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)
vg1128896330 G A -0.03 -0.05 -0.02 -0.03 -0.02 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1128896330 NA 3.50E-09 mr1342 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
vg1128896330 NA 3.05E-11 mr1626 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
vg1128896330 NA 4.77E-06 mr1020_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
vg1128896330 NA 1.72E-07 mr1030_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
vg1128896330 NA 1.26E-07 mr1321_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
vg1128896330 NA 6.72E-07 mr1517_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
vg1128896330 NA 2.63E-08 mr1576_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
vg1128896330 1.42E-06 NA mr1994_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
vg1128896330 6.24E-06 9.69E-08 mr1994_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