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Detailed information for vg0323155815:

Variant ID: vg0323155815 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 23155815
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CCGTGCCCGTGTCTCCCAGGTGCGGGCGTGCACGCCGCCACCCGCCGGGATCCCCTCCCTCTCGTTTTTGCCATCCCATCCCGCCGGGCCTGCTTGACCC[C/T]
GACGCCTCCTTCCTCGAGCTCTCCCAGGTCGGAAACGCCGGCCGCCGCGCCAACCACCGGGGCTCACCCCAAGACGCCGGCGAGGCCCTCCTGCTCCAAG

Reverse complement sequence

CTTGGAGCAGGAGGGCCTCGCCGGCGTCTTGGGGTGAGCCCCGGTGGTTGGCGCGGCGGCCGGCGTTTCCGACCTGGGAGAGCTCGAGGAAGGAGGCGTC[G/A]
GGGTCAAGCAGGCCCGGCGGGATGGGATGGCAAAAACGAGAGGGAGGGGATCCCGGCGGGTGGCGGCGTGCACGCCCGCACCTGGGAGACACGGGCACGG

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 94.30% 1.80% 1.57% 2.29% NA
All Indica  2759 97.60% 0.50% 1.01% 0.87% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 27.50% 25.70% 17.10% 29.74% NA
Indica I  595 99.70% 0.00% 0.17% 0.17% NA
Indica II  465 99.10% 0.00% 0.65% 0.22% NA
Indica III  913 97.60% 0.10% 0.77% 1.53% NA
Indica Intermediate  786 95.20% 1.70% 2.16% 1.02% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 97.90% 2.10% 0.00% 0.00% NA
Intermediate  90 94.40% 1.10% 0.00% 4.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0323155815 C -> T LOC_Os03g41662.1 synonymous_variant ; p.Ser95Ser; LOW synonymous_codon Average:86.694; most accessible tissue: Zhenshan97 young leaf, score: 94.791 N N N N
vg0323155815 C -> DEL LOC_Os03g41662.1 N frameshift_variant Average:86.694; most accessible tissue: Zhenshan97 young leaf, score: 94.791 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)
vg0323155815 C T -0.01 -0.01 -0.02 -0.01 -0.02 -0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0323155815 9.34E-06 8.83E-12 mr1471 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
vg0323155815 NA 7.66E-10 mr1722 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
vg0323155815 NA 1.19E-06 mr1735 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
vg0323155815 NA 7.48E-07 mr1808 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
vg0323155815 NA 2.43E-10 mr1047_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
vg0323155815 3.69E-07 NA mr1134_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
vg0323155815 NA 6.45E-12 mr1409_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
vg0323155815 NA 5.89E-08 mr1582_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
vg0323155815 NA 4.24E-08 mr1642_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
vg0323155815 NA 1.47E-06 mr1762_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
vg0323155815 NA 6.39E-08 mr1808_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
vg0323155815 NA 7.71E-07 mr1815_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