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Detailed information for vg0105080826:

Variant ID: vg0105080826 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 5080826
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: 112. )

Flanking Sequence (100 bp) in Reference Genome:


ACAATAGTGATGCCGGGTTGATGCAGTCGTTGTAGTCGTAGATGACGTGATCGATGCCGTCGTCGGTGACGCGGTCGTTGCCATCGTAAAGAACGCGGTC[G/A]
ATGTTATTGATGAAGCGTCTTGCAGATTAATCTGTTAGAGGACGCGGGATGTCCATCCTTGTGGACAAGTGGCGGCGGCGTGTTTCCCTTGTTGATGAAG

Reverse complement sequence

CTTCATCAACAAGGGAAACACGCCGCCGCCACTTGTCCACAAGGATGGACATCCCGCGTCCTCTAACAGATTAATCTGCAAGACGCTTCATCAATAACAT[C/T]
GACCGCGTTCTTTACGATGGCAACGACCGCGTCACCGACGACGGCATCGATCACGTCATCTACGACTACAACGACTGCATCAACCCGGCATCACTATTGT

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 83.10% 16.20% 0.55% 0.11% NA
All Indica  2759 77.00% 22.90% 0.07% 0.04% NA
All Japonica  1512 99.20% 0.80% 0.00% 0.00% NA
Aus  269 46.50% 43.10% 8.92% 1.49% NA
Indica I  595 27.60% 72.30% 0.17% 0.00% NA
Indica II  465 97.80% 2.20% 0.00% 0.00% NA
Indica III  913 97.80% 2.20% 0.00% 0.00% NA
Indica Intermediate  786 77.90% 21.90% 0.13% 0.13% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 98.00% 2.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 97.90% 2.10% 0.00% 0.00% NA
Intermediate  90 94.40% 5.60% 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
vg0105080826 G -> A LOC_Os01g09810-LOC_Os01g09830 intergenic_region ; MODIFIER silent_mutation Average:63.223; most accessible tissue: Minghui63 root, score: 90.092 N N N N
vg0105080826 G -> DEL N N silent_mutation Average:63.223; most accessible tissue: Minghui63 root, score: 90.092 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)
vg0105080826 G A -0.01 -0.02 -0.02 -0.01 -0.02 -0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0105080826 NA 2.59E-07 mr1662 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
vg0105080826 NA 4.18E-06 mr1662 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
vg0105080826 NA 2.15E-07 mr1745 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
vg0105080826 NA 6.72E-06 mr1295_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
vg0105080826 NA 1.42E-11 mr1482_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
vg0105080826 NA 2.01E-06 mr1482_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
vg0105080826 NA 5.11E-09 mr1565_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
vg0105080826 NA 3.79E-09 mr1598_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
vg0105080826 NA 8.84E-08 mr1748_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