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Detailed information for vg0322441125:

Variant ID: vg0322441125 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 22441125
Reference Allele: CAlternative Allele: T
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GGGATAGGAATTTAGGAGATCGGGGATGGAGACCTTCAAGTGTACGATGCAGGCAAGGAGGCGGTCTTCGTGGTGGGACGGGCGTAGAGGAGGCGGCCGA[C/T]
AGCGACAGGGTTGGCGCGACGGAGTCTTGGCGGCATGGACCTCGGTGACTCATGTGTAGGGTATGGCGACGGGGACGGAGATCCTGACCAGCGAAGGAGA

Reverse complement sequence

TCTCCTTCGCTGGTCAGGATCTCCGTCCCCGTCGCCATACCCTACACATGAGTCACCGAGGTCCATGCCGCCAAGACTCCGTCGCGCCAACCCTGTCGCT[G/A]
TCGGCCGCCTCCTCTACGCCCGTCCCACCACGAAGACCGCCTCCTTGCCTGCATCGTACACTTGAAGGTCTCCATCCCCGATCTCCTAAATTCCTATCCC

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 58.70% 41.20% 0.04% 0.13% NA
All Indica  2759 96.80% 3.10% 0.00% 0.11% NA
All Japonica  1512 0.80% 99.10% 0.00% 0.07% NA
Aus  269 19.70% 80.30% 0.00% 0.00% NA
Indica I  595 98.70% 1.30% 0.00% 0.00% NA
Indica II  465 97.20% 2.80% 0.00% 0.00% NA
Indica III  913 96.90% 3.00% 0.00% 0.11% NA
Indica Intermediate  786 94.90% 4.80% 0.00% 0.25% NA
Temperate Japonica  767 0.40% 99.50% 0.00% 0.13% NA
Tropical Japonica  504 1.40% 98.60% 0.00% 0.00% NA
Japonica Intermediate  241 0.80% 99.20% 0.00% 0.00% NA
VI/Aromatic  96 3.10% 96.90% 0.00% 0.00% NA
Intermediate  90 38.90% 56.70% 2.22% 2.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0322441125 C -> T LOC_Os03g40380.1 upstream_gene_variant ; 35.0bp to feature; MODIFIER silent_mutation Average:82.962; most accessible tissue: Zhenshan97 flower, score: 93.511 N N N N
vg0322441125 C -> T LOC_Os03g40390.1 upstream_gene_variant ; 2148.0bp to feature; MODIFIER silent_mutation Average:82.962; most accessible tissue: Zhenshan97 flower, score: 93.511 N N N N
vg0322441125 C -> T LOC_Os03g40400.1 upstream_gene_variant ; 4839.0bp to feature; MODIFIER silent_mutation Average:82.962; most accessible tissue: Zhenshan97 flower, score: 93.511 N N N N
vg0322441125 C -> T LOC_Os03g40370-LOC_Os03g40380 intergenic_region ; MODIFIER silent_mutation Average:82.962; most accessible tissue: Zhenshan97 flower, score: 93.511 N N N N
vg0322441125 C -> DEL N N silent_mutation Average:82.962; most accessible tissue: Zhenshan97 flower, score: 93.511 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)
vg0322441125 C T -0.25 -0.18 -0.15 -0.2 -0.22 -0.21

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0322441125 NA 3.74E-28 mr1037 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
vg0322441125 NA 1.94E-47 mr1109 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
vg0322441125 NA 1.06E-15 mr1156 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
vg0322441125 NA 1.82E-14 mr1261 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
vg0322441125 NA 1.62E-11 mr1657 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
vg0322441125 NA 1.67E-57 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
vg0322441125 1.02E-07 1.99E-92 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
vg0322441125 NA 1.82E-41 mr1721 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
vg0322441125 NA 2.23E-35 mr1828 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
vg0322441125 NA 9.66E-12 mr1914 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
vg0322441125 NA 6.09E-32 mr1037_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
vg0322441125 NA 7.34E-60 mr1109_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
vg0322441125 NA 9.23E-37 mr1251_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
vg0322441125 NA 1.63E-21 mr1255_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
vg0322441125 NA 2.37E-28 mr1270_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
vg0322441125 NA 4.87E-24 mr1316_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
vg0322441125 NA 1.20E-11 mr1377_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
vg0322441125 NA 5.38E-37 mr1435_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
vg0322441125 NA 3.89E-25 mr1551_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
vg0322441125 1.39E-08 5.50E-118 mr1718_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
vg0322441125 NA 1.40E-15 mr1720_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
vg0322441125 NA 8.52E-56 mr1721_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
vg0322441125 NA 2.88E-15 mr1744_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
vg0322441125 NA 4.84E-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
vg0322441125 4.82E-06 NA mr1750_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
vg0322441125 NA 1.76E-06 mr1925_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
vg0322441125 NA 7.01E-16 mr1938_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