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Detailed information for vg0909674309:

Variant ID: vg0909674309 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 9674309
Reference Allele: AAlternative Allele: T
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 76. )

Flanking Sequence (100 bp) in Reference Genome:


CCGGCTAATTCCGAAAATTAAATTGAAATTGCAGAAGGAATTCTTCTGGACTAAAGAAAGGGAAGAGATTGGCTTTCCGAAGAGCATCCATTACCTTCTG[A/T]
GCATAGCTGCCCCCATCGAACTGCTCCTTGGAAGAGTAGTACCCATCAACGATATCTTCGATGTCGTAAGCCAGGGACTTGATCTGGCCGAGCCAGTGTC

Reverse complement sequence

GACACTGGCTCGGCCAGATCAAGTCCCTGGCTTACGACATCGAAGATATCGTTGATGGGTACTACTCTTCCAAGGAGCAGTTCGATGGGGGCAGCTATGC[T/A]
CAGAAGGTAATGGATGCTCTTCGGAAAGCCAATCTCTTCCCTTTCTTTAGTCCAGAAGAATTCCTTCTGCAATTTCAATTTAATTTTCGGAATTAGCCGG

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 73.30% 26.60% 0.15% 0.00% NA
All Indica  2759 75.20% 24.70% 0.14% 0.00% NA
All Japonica  1512 78.80% 21.10% 0.13% 0.00% NA
Aus  269 32.70% 67.30% 0.00% 0.00% NA
Indica I  595 82.70% 17.10% 0.17% 0.00% NA
Indica II  465 79.80% 19.80% 0.43% 0.00% NA
Indica III  913 68.00% 32.00% 0.00% 0.00% NA
Indica Intermediate  786 75.10% 24.80% 0.13% 0.00% NA
Temperate Japonica  767 81.90% 17.90% 0.26% 0.00% NA
Tropical Japonica  504 74.60% 25.40% 0.00% 0.00% NA
Japonica Intermediate  241 77.60% 22.40% 0.00% 0.00% NA
VI/Aromatic  96 50.00% 50.00% 0.00% 0.00% NA
Intermediate  90 68.90% 30.00% 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
vg0909674309 A -> T LOC_Os09g15840.1 synonymous_variant ; p.Ala103Ala; LOW synonymous_codon Average:86.866; most accessible tissue: Zhenshan97 flower, score: 95.196 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)
vg0909674309 A T -0.03 -0.01 -0.02 -0.02 0.01 0.03

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0909674309 NA 2.52E-06 mr1386_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