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Detailed information for vg0403648569:

Variant ID: vg0403648569 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 3648569
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: 0.05, others allele: 0.00, population size: 99. )

Flanking Sequence (100 bp) in Reference Genome:


AGGACACCAAGCTCTGGCTCCGACACTTGGTTTCTCTCGTTGTGCAGGTATCTGGCACTGCATATGTCCTCTATAAACAATTCAGCGGCAGCCATAATTC[G/A]
CTCCGGCTAGCCGCTGTCTTGATGTTCACCGTAGGTGTTATCAAGTATGGGGAAAGGACATGGGTGCTTAGGTGTGGCAACATCGACACCATCCGGAGTT

Reverse complement sequence

AACTCCGGATGGTGTCGATGTTGCCACACCTAAGCACCCATGTCCTTTCCCCATACTTGATAACACCTACGGTGAACATCAAGACAGCGGCTAGCCGGAG[C/T]
GAATTATGGCTGCCGCTGAATTGTTTATAGAGGACATATGCAGTGCCAGATACCTGCACAACGAGAGAAACCAAGTGTCGGAGCCAGAGCTTGGTGTCCT

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 50.40% 32.70% 1.50% 15.43% NA
All Indica  2759 76.30% 15.60% 0.94% 7.21% NA
All Japonica  1512 13.00% 62.40% 0.99% 23.61% NA
Aus  269 10.40% 50.90% 4.83% 33.83% NA
Indica I  595 93.30% 4.90% 0.50% 1.34% NA
Indica II  465 66.00% 20.60% 1.08% 12.26% NA
Indica III  913 76.70% 15.80% 0.77% 6.79% NA
Indica Intermediate  786 69.00% 20.50% 1.40% 9.16% NA
Temperate Japonica  767 1.80% 92.70% 0.26% 5.22% NA
Tropical Japonica  504 24.00% 21.20% 2.38% 52.38% NA
Japonica Intermediate  241 25.30% 52.30% 0.41% 21.99% NA
VI/Aromatic  96 9.40% 9.40% 13.54% 67.71% NA
Intermediate  90 47.80% 28.90% 4.44% 18.89% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0403648569 G -> DEL LOC_Os04g06910.1 N frameshift_variant Average:78.006; most accessible tissue: Zhenshan97 panicle, score: 91.206 N N N N
vg0403648569 G -> A LOC_Os04g06910.1 synonymous_variant ; p.Ser118Ser; LOW synonymous_codon Average:78.006; most accessible tissue: Zhenshan97 panicle, score: 91.206 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)
vg0403648569 G A 0.02 0.0 0.0 0.01 0.02 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0403648569 3.16E-07 2.34E-07 mr1035 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
vg0403648569 NA 4.76E-06 mr1332 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
vg0403648569 6.49E-06 3.77E-06 mr1626 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
vg0403648569 1.45E-06 NA mr1631 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
vg0403648569 5.45E-07 1.13E-06 mr1631 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