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Detailed information for vg1010655699:

Variant ID: vg1010655699 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 10655699
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.02, others allele: 0.00, population size: 124. )

Flanking Sequence (100 bp) in Reference Genome:


ATGGAGTGGCGGCCAGCGGTGGGAGGTGTGGGATGCGATAGAAGCTGCGGACGTCGATAGCCTTGGGGAGCCACGATGCGATCCTTGGTTGCGGCAGCAG[C/T]
AACGTGGTAGAAGTAGGAGCAAGCCACGACGACGCAGTGGTCCTGCAATATGGTACTCCCTTCGTCCCAAAATGTAATAACTTTTAACTCTCAAGATTTA

Reverse complement sequence

TAAATCTTGAGAGTTAAAAGTTATTACATTTTGGGACGAAGGGAGTACCATATTGCAGGACCACTGCGTCGTCGTGGCTTGCTCCTACTTCTACCACGTT[G/A]
CTGCTGCCGCAACCAAGGATCGCATCGTGGCTCCCCAAGGCTATCGACGTCCGCAGCTTCTATCGCATCCCACACCTCCCACCGCTGGCCGCCACTCCAT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 66.30% 33.60% 0.06% 0.00% NA
All Indica  2759 43.60% 56.30% 0.07% 0.00% NA
All Japonica  1512 99.30% 0.70% 0.00% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 26.60% 73.30% 0.17% 0.00% NA
Indica II  465 30.10% 69.90% 0.00% 0.00% NA
Indica III  913 58.40% 41.60% 0.00% 0.00% NA
Indica Intermediate  786 47.30% 52.50% 0.13% 0.00% NA
Temperate Japonica  767 99.50% 0.50% 0.00% 0.00% NA
Tropical Japonica  504 99.40% 0.60% 0.00% 0.00% NA
Japonica Intermediate  241 98.80% 1.20% 0.00% 0.00% NA
VI/Aromatic  96 97.90% 1.00% 1.04% 0.00% NA
Intermediate  90 74.40% 25.60% 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
vg1010655699 C -> T LOC_Os10g21020.1 upstream_gene_variant ; 727.0bp to feature; MODIFIER silent_mutation Average:82.545; most accessible tissue: Minghui63 flag leaf, score: 91.489 N N N N
vg1010655699 C -> T LOC_Os10g21040.1 upstream_gene_variant ; 3170.0bp to feature; MODIFIER silent_mutation Average:82.545; most accessible tissue: Minghui63 flag leaf, score: 91.489 N N N N
vg1010655699 C -> T LOC_Os10g21020-LOC_Os10g21040 intergenic_region ; MODIFIER silent_mutation Average:82.545; most accessible tissue: Minghui63 flag leaf, score: 91.489 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)
vg1010655699 C T -0.09 -0.16 -0.06 -0.01 -0.05 -0.05

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1010655699 8.91E-06 6.16E-43 mr1026 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
vg1010655699 NA 8.04E-17 mr1026 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
vg1010655699 NA 4.16E-13 mr1118 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
vg1010655699 6.19E-06 8.26E-43 mr1161 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
vg1010655699 NA 2.22E-17 mr1161 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
vg1010655699 NA 6.86E-12 mr1495 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
vg1010655699 NA 6.38E-15 mr1118_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
vg1010655699 1.49E-06 1.88E-18 mr1118_2 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
vg1010655699 NA 2.26E-41 mr1161_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
vg1010655699 NA 1.46E-16 mr1161_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
vg1010655699 NA 1.88E-07 mr1212_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
vg1010655699 7.71E-06 NA mr1495_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
vg1010655699 2.10E-07 4.07E-18 mr1495_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
vg1010655699 NA 1.30E-06 mr1496_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
vg1010655699 NA 4.58E-07 mr1936_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