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Detailed information for vg0324070014:

Variant ID: vg0324070014 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 24070014
Reference Allele: AAlternative Allele: C
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTGGTGGAAATGTGCTATTGTGCCAACCTCTCCCTGCCTTCTACTGCTACGCCTCAGCGAGCAGCCATGCTTCGCGTACGGCGGCCCTAGCGCACGTGAC[A/C]
CCATTCACCGCACGCGATCAGAGCTTCAACACTTGGAACGTTTGTCTAAAAGTTTACTACAGTATGTACATAGTTGTCTAGTACTCCATATATCACACAG

Reverse complement sequence

CTGTGTGATATATGGAGTACTAGACAACTATGTACATACTGTAGTAAACTTTTAGACAAACGTTCCAAGTGTTGAAGCTCTGATCGCGTGCGGTGAATGG[T/G]
GTCACGTGCGCTAGGGCCGCCGTACGCGAAGCATGGCTGCTCGCTGAGGCGTAGCAGTAGAAGGCAGGGAGAGGTTGGCACAATAGCACATTTCCACCAA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 58.70% 40.50% 0.21% 0.63% NA
All Indica  2759 97.30% 2.10% 0.22% 0.36% NA
All Japonica  1512 0.80% 99.10% 0.00% 0.07% NA
Aus  269 11.20% 88.50% 0.37% 0.00% NA
Indica I  595 99.00% 0.30% 0.50% 0.17% NA
Indica II  465 98.10% 1.70% 0.22% 0.00% NA
Indica III  913 98.80% 0.90% 0.22% 0.11% NA
Indica Intermediate  786 93.90% 5.10% 0.00% 1.02% NA
Temperate Japonica  767 0.50% 99.50% 0.00% 0.00% NA
Tropical Japonica  504 1.00% 99.00% 0.00% 0.00% NA
Japonica Intermediate  241 1.20% 98.30% 0.00% 0.41% NA
VI/Aromatic  96 4.20% 78.10% 1.04% 16.67% NA
Intermediate  90 45.60% 48.90% 2.22% 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
vg0324070014 A -> C LOC_Os03g43140-LOC_Os03g43150 intergenic_region ; MODIFIER silent_mutation Average:80.488; most accessible tissue: Zhenshan97 panicle, score: 95.654 N N N N
vg0324070014 A -> DEL N N silent_mutation Average:80.488; most accessible tissue: Zhenshan97 panicle, score: 95.654 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)
vg0324070014 A C 0.0 0.01 -0.01 0.01 0.05 0.05

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0324070014 NA 5.86E-49 mr1063 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
vg0324070014 NA 1.67E-41 mr1458 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
vg0324070014 NA 1.55E-41 mr1509 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
vg0324070014 NA 4.29E-10 mr1524 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
vg0324070014 NA 2.57E-49 mr1558 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
vg0324070014 NA 3.92E-59 mr1671 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
vg0324070014 NA 1.81E-81 mr1718 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
vg0324070014 NA 2.01E-31 mr1745 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
vg0324070014 NA 2.87E-29 mr1793 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
vg0324070014 NA 4.65E-23 mr1841 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
vg0324070014 NA 9.70E-51 mr1063_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
vg0324070014 NA 4.60E-12 mr1151_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
vg0324070014 NA 4.83E-09 mr1198_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
vg0324070014 NA 6.95E-22 mr1401_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
vg0324070014 NA 6.01E-51 mr1509_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
vg0324070014 NA 8.18E-65 mr1558_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
vg0324070014 NA 2.05E-32 mr1571_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
vg0324070014 NA 2.81E-78 mr1671_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
vg0324070014 NA 8.97E-22 mr1698_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
vg0324070014 NA 7.18E-40 mr1745_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
vg0324070014 NA 1.12E-28 mr1825_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
vg0324070014 NA 6.72E-20 mr1922_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
vg0324070014 NA 5.00E-21 mr1924_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