Search for Variation information by Variation ID:

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

Detailed information for vg0107054597:

Variant ID: vg0107054597 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 7054597
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: 295. )

Flanking Sequence (100 bp) in Reference Genome:


TTTTCAACCACTCTAGATCCCACGCTCTCACCGCTAACGCCTGACTTTGTCCACCAGCCTAGCCCTCTTGCCCATAGGTTCATGATCCAACCGTTGTTGT[G/A]
AACATAGAAAAAAAGATCCTCTAAAATATTGCCCTCTAACTTTGTAGGTCTTACATTGAGCGGGTCCATATGCATAATTGCATATGCATGTGACCCACTA

Reverse complement sequence

TAGTGGGTCACATGCATATGCAATTATGCATATGGACCCGCTCAATGTAAGACCTACAAAGTTAGAGGGCAATATTTTAGAGGATCTTTTTTTCTATGTT[C/T]
ACAACAACGGTTGGATCATGAACCTATGGGCAAGAGGGCTAGGCTGGTGGACAAAGTCAGGCGTTAGCGGTGAGAGCGTGGGATCTAGAGTGGTTGAAAA

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 90.30% 8.20% 0.00% 1.46% NA
All Indica  2759 98.40% 0.00% 0.00% 1.56% NA
All Japonica  1512 73.30% 25.00% 0.00% 1.72% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 96.10% 0.00% 0.00% 3.87% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.70% 0.00% 0.00% 0.33% NA
Indica Intermediate  786 97.70% 0.10% 0.00% 2.16% NA
Temperate Japonica  767 67.70% 32.30% 0.00% 0.00% NA
Tropical Japonica  504 80.40% 15.10% 0.00% 4.56% NA
Japonica Intermediate  241 76.30% 22.40% 0.00% 1.24% NA
VI/Aromatic  96 91.70% 8.30% 0.00% 0.00% NA
Intermediate  90 97.80% 2.20% 0.00% 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
vg0107054597 G -> A LOC_Os01g12740.1 downstream_gene_variant ; 3720.0bp to feature; MODIFIER silent_mutation Average:95.519; most accessible tissue: Minghui63 flag leaf, score: 98.622 N N N N
vg0107054597 G -> A LOC_Os01g12750.1 intron_variant ; MODIFIER silent_mutation Average:95.519; most accessible tissue: Minghui63 flag leaf, score: 98.622 N N N N
vg0107054597 G -> DEL N N silent_mutation Average:95.519; most accessible tissue: Minghui63 flag leaf, score: 98.622 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)
vg0107054597 G A 0.01 0.03 0.01 0.01 0.03 0.03

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0107054597 NA 8.42E-06 mr1123 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
vg0107054597 NA 1.18E-06 mr1240 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
vg0107054597 NA 9.29E-07 mr1496 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
vg0107054597 4.07E-08 NA mr1679 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
vg0107054597 6.81E-07 6.45E-12 mr1691 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
vg0107054597 NA 5.62E-07 mr1691 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
vg0107054597 6.55E-06 2.44E-12 mr1693 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
vg0107054597 NA 4.05E-07 mr1693 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
vg0107054597 NA 9.89E-06 mr1720 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
vg0107054597 NA 9.11E-07 mr1936 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
vg0107054597 NA 1.80E-07 mr1691_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
vg0107054597 3.65E-06 NA mr1733_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