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Detailed information for vg0102710977:

Variant ID: vg0102710977 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 2710977
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.74, A: 0.25, others allele: 0.00, population size: 186. )

Flanking Sequence (100 bp) in Reference Genome:


CATGTAAATACGACCAAACCCTTCCAAAGAATGAGAAGATAACGAAGTGCAGGAGAGCCACTACAAGTACTACTCCTTTAACACATCAACAAACACAACC[A/G]
TAAAACGGGAAATTTTGACGGGATCATTGCACTTACTCTTGGCATAGATGGCATCCTGCAGATCCGCGACCTTAGCCTGCAAAAGAAAAGAAAACAAGAA

Reverse complement sequence

TTCTTGTTTTCTTTTCTTTTGCAGGCTAAGGTCGCGGATCTGCAGGATGCCATCTATGCCAAGAGTAAGTGCAATGATCCCGTCAAAATTTCCCGTTTTA[T/C]
GGTTGTGTTTGTTGATGTGTTAAAGGAGTAGTACTTGTAGTGGCTCTCCTGCACTTCGTTATCTTCTCATTCTTTGGAAGGGTTTGGTCGTATTTACATG

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 71.70% 28.30% 0.04% 0.00% NA
All Indica  2759 86.30% 13.70% 0.04% 0.00% NA
All Japonica  1512 59.10% 40.90% 0.07% 0.00% NA
Aus  269 13.00% 87.00% 0.00% 0.00% NA
Indica I  595 92.40% 7.60% 0.00% 0.00% NA
Indica II  465 91.60% 8.40% 0.00% 0.00% NA
Indica III  913 80.90% 18.90% 0.11% 0.00% NA
Indica Intermediate  786 84.60% 15.40% 0.00% 0.00% NA
Temperate Japonica  767 33.80% 66.10% 0.13% 0.00% NA
Tropical Japonica  504 93.10% 6.90% 0.00% 0.00% NA
Japonica Intermediate  241 68.50% 31.50% 0.00% 0.00% NA
VI/Aromatic  96 11.50% 88.50% 0.00% 0.00% NA
Intermediate  90 76.70% 23.30% 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
vg0102710977 A -> G LOC_Os01g05680.1 upstream_gene_variant ; 2435.0bp to feature; MODIFIER silent_mutation Average:84.083; most accessible tissue: Minghui63 flag leaf, score: 93.996 N N N N
vg0102710977 A -> G LOC_Os01g05670.1 intron_variant ; MODIFIER silent_mutation Average:84.083; most accessible tissue: Minghui63 flag leaf, score: 93.996 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)
vg0102710977 A G -0.01 0.0 0.0 0.0 -0.01 -0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0102710977 NA 4.21E-06 mr1347 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
vg0102710977 NA 7.27E-08 mr1364 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
vg0102710977 NA 4.16E-10 mr1443 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
vg0102710977 NA 1.55E-09 mr1347_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
vg0102710977 NA 1.59E-06 mr1354_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
vg0102710977 NA 1.40E-07 mr1567_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
vg0102710977 NA 1.87E-06 mr1829_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
vg0102710977 NA 2.19E-06 mr1902_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