Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0909674408:

Variant ID: vg0909674408 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 9674408
Reference Allele: TAlternative Allele: G
Primary Allele: TSecondary Allele: G

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 90. )

Flanking Sequence (100 bp) in Reference Genome:


GAGCATAGCTGCCCCCATCGAACTGCTCCTTGGAAGAGTAGTACCCATCAACGATATCTTCGATGTCGTAAGCCAGGGACTTGATCTGGCCGAGCCAGTG[T/G]
CGCAGGTTGGCCCTGTCGCTTCCGAAGGAGTTGTTCTCGGCGTTTTTCAGAAGGGTTTCCAGGTACACCAAGGTATCCTTGATGCCCTCCAAATCGTCGC

Reverse complement sequence

GCGACGATTTGGAGGGCATCAAGGATACCTTGGTGTACCTGGAAACCCTTCTGAAAAACGCCGAGAACAACTCCTTCGGAAGCGACAGGGCCAACCTGCG[A/C]
CACTGGCTCGGCCAGATCAAGTCCCTGGCTTACGACATCGAAGATATCGTTGATGGGTACTACTCTTCCAAGGAGCAGTTCGATGGGGGCAGCTATGCTC

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 77.40% 22.50% 0.08% 0.06% NA
All Indica  2759 76.40% 23.50% 0.04% 0.07% NA
All Japonica  1512 78.80% 21.10% 0.07% 0.07% NA
Aus  269 72.90% 27.10% 0.00% 0.00% NA
Indica I  595 82.90% 17.00% 0.00% 0.17% NA
Indica II  465 80.00% 19.80% 0.22% 0.00% NA
Indica III  913 68.90% 31.10% 0.00% 0.00% NA
Indica Intermediate  786 78.10% 21.80% 0.00% 0.13% NA
Temperate Japonica  767 81.90% 18.00% 0.13% 0.00% NA
Tropical Japonica  504 74.40% 25.40% 0.00% 0.20% NA
Japonica Intermediate  241 78.00% 22.00% 0.00% 0.00% NA
VI/Aromatic  96 91.70% 8.30% 0.00% 0.00% NA
Intermediate  90 81.10% 16.70% 2.22% 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
vg0909674408 T -> G LOC_Os09g15840.1 synonymous_variant ; p.Arg70Arg; LOW synonymous_codon Average:87.517; most accessible tissue: Minghui63 panicle, score: 94.638 N N N N
vg0909674408 T -> DEL LOC_Os09g15840.1 N frameshift_variant Average:87.517; most accessible tissue: Minghui63 panicle, score: 94.638 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)
vg0909674408 T G 0.09 0.09 0.09 0.07 0.08 0.09

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0909674408 NA 2.41E-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