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Detailed information for vg0717185752:

Variant ID: vg0717185752 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 17185752
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 331. )

Flanking Sequence (100 bp) in Reference Genome:


ATATGTGCCAAGGCTGTGGGCCATGGACGAGGTGTCAAAAGCGAGGGCCCTGTTACCGAAGATCACTGAATTTGCGTCCTTTATTGGGTCATCACCTGAG[G/A]
GATGCGTTGTGACATCATGTCTAGTCTATCTATCAACAATGGGGCTCCGTCCGCTCACCATAGTGCATAATCGATGTATCTCTAGTGCAGTATAAGGAGG

Reverse complement sequence

CCTCCTTATACTGCACTAGAGATACATCGATTATGCACTATGGTGAGCGGACGGAGCCCCATTGTTGATAGATAGACTAGACATGATGTCACAACGCATC[C/T]
CTCAGGTGATGACCCAATAAAGGACGCAAATTCAGTGATCTTCGGTAACAGGGCCCTCGCTTTTGACACCTCGTCCATGGCCCACAGCCTTGGCACATAT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 93.80% 5.40% 0.76% 0.00% NA
All Indica  2759 99.70% 0.30% 0.04% 0.00% NA
All Japonica  1512 82.10% 15.70% 2.18% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.10% 0.60% 0.22% 0.00% NA
Indica III  913 99.80% 0.20% 0.00% 0.00% NA
Indica Intermediate  786 99.70% 0.30% 0.00% 0.00% NA
Temperate Japonica  767 92.20% 5.60% 2.22% 0.00% NA
Tropical Japonica  504 73.20% 25.40% 1.39% 0.00% NA
Japonica Intermediate  241 68.50% 27.80% 3.73% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 86.70% 11.10% 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
vg0717185752 G -> A LOC_Os07g29310.1 upstream_gene_variant ; 921.0bp to feature; MODIFIER silent_mutation Average:86.634; most accessible tissue: Zhenshan97 panicle, score: 96.769 N N N N
vg0717185752 G -> A LOC_Os07g29300-LOC_Os07g29310 intergenic_region ; MODIFIER silent_mutation Average:86.634; most accessible tissue: Zhenshan97 panicle, score: 96.769 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)
vg0717185752 G A -0.05 -0.1 -0.06 -0.04 -0.06 -0.11

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0717185752 NA 4.47E-07 mr1229 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
vg0717185752 3.43E-10 NA mr1238 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
vg0717185752 9.10E-06 4.30E-06 mr1238 Jap_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
vg0717185752 NA 6.35E-06 mr1900 Jap_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
vg0717185752 7.08E-10 NA mr1238_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
vg0717185752 NA 4.61E-06 mr1238_2 Jap_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
vg0717185752 3.32E-07 NA mr1484_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
vg0717185752 1.18E-07 NA mr1841_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
vg0717185752 2.37E-09 NA mr1900_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
vg0717185752 4.72E-06 1.02E-06 mr1900_2 Jap_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
vg0717185752 3.98E-08 NA mr1945_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