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Detailed information for vg0712717909:

Variant ID: vg0712717909 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 12717909
Reference Allele: CAlternative Allele: A
Primary Allele: ASecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.63, A: 0.36, others allele: 0.00, population size: 30. )

Flanking Sequence (100 bp) in Reference Genome:


ACAGCAAAAACTTGTGGGGGGGGGGAGTTGTTTTCTATTCATACTGGCAATTCAAATTAATGAAATCACACAGAAAACTATGTCTTACGAGCAATGTCAT[C/A]
ACAACATTACAGTGAATCAGGTTAGCCCATGGCATAAGGGAACTATAGGGTAGGGAGCCCAGAGCAATACAGGGAGCAGGCAGAACAATAAAATAGAGAA

Reverse complement sequence

TTCTCTATTTTATTGTTCTGCCTGCTCCCTGTATTGCTCTGGGCTCCCTACCCTATAGTTCCCTTATGCCATGGGCTAACCTGATTCACTGTAATGTTGT[G/T]
ATGACATTGCTCGTAAGACATAGTTTTCTGTGTGATTTCATTAATTTGAATTGCCAGTATGAATAGAAAACAACTCCCCCCCCCCACAAGTTTTTGCTGT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 59.60% 31.20% 8.34% 0.93% NA
All Indica  2759 92.80% 5.20% 1.59% 0.40% NA
All Japonica  1512 1.90% 78.80% 17.53% 1.79% NA
Aus  269 62.80% 32.30% 4.46% 0.37% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 92.90% 6.90% 0.00% 0.22% NA
Indica III  913 93.60% 6.10% 0.11% 0.11% NA
Indica Intermediate  786 86.30% 7.10% 5.47% 1.15% NA
Temperate Japonica  767 2.10% 65.60% 29.20% 3.13% NA
Tropical Japonica  504 0.80% 98.20% 0.79% 0.20% NA
Japonica Intermediate  241 3.70% 80.10% 15.35% 0.83% NA
VI/Aromatic  96 17.70% 8.30% 71.88% 2.08% NA
Intermediate  90 44.40% 47.80% 4.44% 3.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0712717909 C -> DEL N N silent_mutation Average:76.419; most accessible tissue: Minghui63 flag leaf, score: 85.151 N N N N
vg0712717909 C -> A LOC_Os07g22590.1 downstream_gene_variant ; 4546.0bp to feature; MODIFIER silent_mutation Average:76.419; most accessible tissue: Minghui63 flag leaf, score: 85.151 N N N N
vg0712717909 C -> A LOC_Os07g22600.1 intron_variant ; MODIFIER silent_mutation Average:76.419; most accessible tissue: Minghui63 flag leaf, score: 85.151 N N N N
vg0712717909 C -> A LOC_Os07g22600.2 intron_variant ; MODIFIER silent_mutation Average:76.419; most accessible tissue: Minghui63 flag leaf, score: 85.151 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)
vg0712717909 C A -0.01 -0.01 -0.01 -0.02 -0.01 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0712717909 NA 1.75E-08 mr1063 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
vg0712717909 NA 2.11E-09 mr1578 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
vg0712717909 NA 2.26E-10 mr1581 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
vg0712717909 NA 1.25E-07 mr1666 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
vg0712717909 NA 2.31E-13 mr1900 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
vg0712717909 NA 1.04E-09 mr1905 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
vg0712717909 NA 5.65E-07 mr1915 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
vg0712717909 NA 8.92E-18 mr1062_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
vg0712717909 NA 8.20E-07 mr1227_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
vg0712717909 NA 6.48E-07 mr1302_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
vg0712717909 NA 1.92E-06 mr1405_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
vg0712717909 NA 1.07E-06 mr1418_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
vg0712717909 NA 4.46E-07 mr1604_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
vg0712717909 NA 2.45E-10 mr1646_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
vg0712717909 NA 2.28E-10 mr1680_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
vg0712717909 NA 5.25E-10 mr1751_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
vg0712717909 NA 3.17E-12 mr1851_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