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Detailed information for vg0826159860:

Variant ID: vg0826159860 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 26159860
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 82. )

Flanking Sequence (100 bp) in Reference Genome:


GGGGATTTTCCTACGCGTTTGGGGGGATTTCTGTTCGTCAATGATTTCTTTGGAGGGCGATTTGGGGTTTTCTACAGGTGGATTCGGCGCGAGGGCATGG[G/A]
GCAGCGAAGAAATGCCCACAGCGCGCGTGCCTCCCTTTTCCCCGGCCGCTCGCGCCCTCGCTGCAACGAAGTATTGCGCCGCTTAGGTAGGGGACGGGAA

Reverse complement sequence

TTCCCGTCCCCTACCTAAGCGGCGCAATACTTCGTTGCAGCGAGGGCGCGAGCGGCCGGGGAAAAGGGAGGCACGCGCGCTGTGGGCATTTCTTCGCTGC[C/T]
CCATGCCCTCGCGCCGAATCCACCTGTAGAAAACCCCAAATCGCCCTCCAAAGAAATCATTGACGAACAGAAATCCCCCCAAACGCGTAGGAAAATCCCC

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 61.30% 38.40% 0.32% 0.00% NA
All Indica  2759 42.00% 57.40% 0.51% 0.00% NA
All Japonica  1512 98.50% 1.40% 0.07% 0.00% NA
Aus  269 35.70% 64.30% 0.00% 0.00% NA
Indica I  595 46.70% 52.90% 0.34% 0.00% NA
Indica II  465 64.30% 35.10% 0.65% 0.00% NA
Indica III  913 26.90% 72.40% 0.66% 0.00% NA
Indica Intermediate  786 42.90% 56.70% 0.38% 0.00% NA
Temperate Japonica  767 99.60% 0.40% 0.00% 0.00% NA
Tropical Japonica  504 98.00% 2.00% 0.00% 0.00% NA
Japonica Intermediate  241 96.30% 3.30% 0.41% 0.00% NA
VI/Aromatic  96 92.70% 7.30% 0.00% 0.00% NA
Intermediate  90 67.80% 32.20% 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
vg0826159860 G -> A LOC_Os08g41420.1 upstream_gene_variant ; 1997.0bp to feature; MODIFIER silent_mutation Average:83.297; most accessible tissue: Zhenshan97 flag leaf, score: 92.554 N N N N
vg0826159860 G -> A LOC_Os08g41430.1 upstream_gene_variant ; 12.0bp to feature; MODIFIER silent_mutation Average:83.297; most accessible tissue: Zhenshan97 flag leaf, score: 92.554 N N N N
vg0826159860 G -> A LOC_Os08g41420-LOC_Os08g41430 intergenic_region ; MODIFIER silent_mutation Average:83.297; most accessible tissue: Zhenshan97 flag leaf, score: 92.554 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)
vg0826159860 G A -0.04 -0.03 -0.04 -0.06 -0.05 -0.06

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0826159860 5.14E-06 5.14E-06 mr1048 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
vg0826159860 NA 3.32E-06 mr1264 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
vg0826159860 NA 8.60E-06 mr1283 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
vg0826159860 3.51E-06 6.10E-07 mr1297 Ind_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
vg0826159860 NA 4.00E-12 mr1307 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
vg0826159860 NA 3.95E-07 mr1315 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
vg0826159860 NA 1.41E-06 mr1392 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
vg0826159860 NA 2.68E-06 mr1433 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
vg0826159860 4.56E-06 8.27E-07 mr1433 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
vg0826159860 NA 2.62E-06 mr1450 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
vg0826159860 NA 2.49E-07 mr1511 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
vg0826159860 NA 5.05E-09 mr1607 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
vg0826159860 4.14E-06 NA mr1649 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
vg0826159860 1.96E-07 3.58E-08 mr1649 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
vg0826159860 NA 1.91E-08 mr1680 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
vg0826159860 NA 3.12E-06 mr1687 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
vg0826159860 1.37E-06 1.37E-06 mr1953 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