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Detailed information for vg0814031551:

Variant ID: vg0814031551 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 14031551
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.94, A: 0.06, others allele: 0.00, population size: 96. )

Flanking Sequence (100 bp) in Reference Genome:


CGACCGTAGGTGGGAGTCGAACCAGTGGCTCCGGCGGGGGTGGTAGCTCCAGGGCACCCGGCCCGAGCCGCGGGCCCGGGGGAGATTCGGCCAACGACCC[G/A]
AAAGGAAAGCGGAAAATGTCCAAATCTCGACCGCCCTCTCCTCCGTGCATAGGGGGCGCCGAGCGCGTGGCGGACCGACCGAAGTTGGACGGAAGAAGAA

Reverse complement sequence

TTCTTCTTCCGTCCAACTTCGGTCGGTCCGCCACGCGCTCGGCGCCCCCTATGCACGGAGGAGAGGGCGGTCGAGATTTGGACATTTTCCGCTTTCCTTT[C/T]
GGGTCGTTGGCCGAATCTCCCCCGGGCCCGCGGCTCGGGCCGGGTGCCCTGGAGCTACCACCCCCGCCGGAGCCACTGGTTCGACTCCCACCTACGGTCG

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 51.80% 43.90% 0.32% 3.94% NA
All Indica  2759 84.60% 10.40% 0.51% 4.49% NA
All Japonica  1512 2.20% 93.70% 0.00% 4.10% NA
Aus  269 16.70% 83.30% 0.00% 0.00% NA
Indica I  595 97.50% 0.80% 0.00% 1.68% NA
Indica II  465 87.50% 8.60% 0.43% 3.44% NA
Indica III  913 78.20% 14.90% 0.88% 6.02% NA
Indica Intermediate  786 80.50% 13.50% 0.51% 5.47% NA
Temperate Japonica  767 2.30% 90.10% 0.00% 7.56% NA
Tropical Japonica  504 1.40% 98.40% 0.00% 0.20% NA
Japonica Intermediate  241 3.30% 95.40% 0.00% 1.24% NA
VI/Aromatic  96 4.20% 94.80% 1.04% 0.00% NA
Intermediate  90 36.70% 63.30% 0.00% 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
vg0814031551 G -> A LOC_Os08g23240.1 synonymous_variant ; p.Pro211Pro; LOW synonymous_codon Average:84.278; most accessible tissue: Minghui63 flag leaf, score: 93.46 N N N N
vg0814031551 G -> DEL LOC_Os08g23240.1 N frameshift_variant Average:84.278; most accessible tissue: Minghui63 flag leaf, score: 93.46 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)
vg0814031551 G A -0.01 -0.02 -0.02 -0.01 -0.01 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0814031551 NA 8.14E-06 mr1134 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
vg0814031551 NA 5.21E-13 mr1657 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
vg0814031551 NA 2.62E-16 mr1870 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
vg0814031551 NA 1.85E-08 mr1134_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
vg0814031551 NA 1.69E-23 mr1422_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
vg0814031551 NA 4.02E-06 mr1504_2 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
vg0814031551 NA 9.66E-07 mr1548_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
vg0814031551 4.30E-06 1.86E-08 mr1672_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
vg0814031551 NA 4.69E-11 mr1734_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
vg0814031551 NA 1.49E-10 mr1782_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
vg0814031551 NA 7.19E-17 mr1870_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