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Detailed information for vg0140756777:

Variant ID: vg0140756777 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 40756777
Reference Allele: TAlternative Allele: C,A
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 309. )

Flanking Sequence (100 bp) in Reference Genome:


CAGATTCTATTACGGAGTGAGACTTTTACCGTCTGTGCCTTTCCTTGTAGCTAGAGTCGTACACGGTAGCCGGACAACAGGGTCGTATGTATATCATTTT[T/C,A]
GTATTTCCTTTTATATGGATCATCTCCTTGCAAAAATGTGTAAACCAATAAGCCCCCAACCTCATGATGGCATTGAGCAGAAGAGTACTTTGGAGCATTG

Reverse complement sequence

CAATGCTCCAAAGTACTCTTCTGCTCAATGCCATCATGAGGTTGGGGGCTTATTGGTTTACACATTTTTGCAAGGAGATGATCCATATAAAAGGAAATAC[A/G,T]
AAAATGATATACATACGACCCTGTTGTCCGGCTACCGTGTACGACTCTAGCTACAAGGAAAGGCACAGACGGTAAAAGTCTCACTCCGTAATAGAATCTG

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 74.50% 25.00% 0.49% 0.00% A: 0.04%
All Indica  2759 99.10% 0.90% 0.00% 0.00% NA
All Japonica  1512 24.10% 74.50% 1.46% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 98.20% 1.80% 0.00% 0.00% NA
Indica II  465 98.70% 1.30% 0.00% 0.00% NA
Indica III  913 99.70% 0.30% 0.00% 0.00% NA
Indica Intermediate  786 99.40% 0.60% 0.00% 0.00% NA
Temperate Japonica  767 8.90% 89.40% 1.69% 0.00% NA
Tropical Japonica  504 36.90% 62.70% 0.40% 0.00% NA
Japonica Intermediate  241 45.60% 51.50% 2.90% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 64.40% 32.20% 1.11% 0.00% A: 2.22%

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0140756777 T -> A LOC_Os01g70350.1 stop_gained ; p.Lys37*; HIGH stop_gained Average:67.099; most accessible tissue: Zhenshan97 panicle, score: 93.845 N N N N
vg0140756777 T -> C LOC_Os01g70350.1 missense_variant ; p.Lys37Glu; MODERATE nonsynonymous_codon ; K37E Average:67.099; most accessible tissue: Zhenshan97 panicle, score: 93.845 unknown unknown DELETERIOUS 0.00

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)
vg0140756777 T A 0.01 0.0 0.0 0.01 0.0 0.01
vg0140756777 T C -0.04 0.0 0.0 0.02 0.05 0.04

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0140756777 NA 7.62E-17 mr1116 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
vg0140756777 NA 4.72E-13 mr1636 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
vg0140756777 NA 9.33E-14 mr1641 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
vg0140756777 NA 2.07E-15 mr1653 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
vg0140756777 NA 2.17E-10 mr1683 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
vg0140756777 3.92E-06 NA mr1691 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
vg0140756777 NA 2.43E-27 mr1617_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
vg0140756777 NA 3.50E-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