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Detailed information for vg0432278118:

Variant ID: vg0432278118 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 32278118
Reference Allele: GAlternative Allele: A,C,T
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.91, A: 0.09, others allele: 0.00, population size: 195. )

Flanking Sequence (100 bp) in Reference Genome:


GTCTTCTTGTTTAGCACTTAACTTACTAGTGAATTATCAGACCCAAATCACTTTTTCCCTTCTCAGGCAGCGGCGGCAAACCAAACAAGCAAAAGTTCAG[G/A,C,T]
CCGCCTGGCCAGGTAACATTCAAGAACTTCTCAGAAGCATGGTGCTCAGGGCATCAACCAAACAGGCCCACAACAGGAGGATAAATTTCCTGGTGTTGCA

Reverse complement sequence

TGCAACACCAGGAAATTTATCCTCCTGTTGTGGGCCTGTTTGGTTGATGCCCTGAGCACCATGCTTCTGAGAAGTTCTTGAATGTTACCTGGCCAGGCGG[C/T,G,A]
CTGAACTTTTGCTTGTTTGGTTTGCCGCCGCTGCCTGAGAAGGGAAAAAGTGATTTGGGTCTGATAATTCACTAGTAAGTTAAGTGCTAAACAAGAAGAC

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 80.50% 18.40% 0.21% 0.89% NA
All Indica  2759 94.00% 5.10% 0.00% 0.91% NA
All Japonica  1512 69.60% 30.30% 0.07% 0.00% NA
Aus  269 24.20% 66.50% 2.97% 6.32% NA
Indica I  595 98.70% 1.30% 0.00% 0.00% NA
Indica II  465 93.30% 6.70% 0.00% 0.00% NA
Indica III  913 93.60% 3.90% 0.00% 2.41% NA
Indica Intermediate  786 91.20% 8.40% 0.00% 0.38% NA
Temperate Japonica  767 92.60% 7.40% 0.00% 0.00% NA
Tropical Japonica  504 47.60% 52.20% 0.20% 0.00% NA
Japonica Intermediate  241 42.70% 57.30% 0.00% 0.00% NA
VI/Aromatic  96 26.00% 74.00% 0.00% 0.00% NA
Intermediate  90 76.70% 22.20% 1.11% 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
vg0432278118 G -> C LOC_Os04g54180.1 upstream_gene_variant ; 1166.0bp to feature; MODIFIER N Average:73.287; most accessible tissue: Zhenshan97 root, score: 86.891 N N N N
vg0432278118 G -> C LOC_Os04g54190.1 downstream_gene_variant ; 29.0bp to feature; MODIFIER N Average:73.287; most accessible tissue: Zhenshan97 root, score: 86.891 N N N N
vg0432278118 G -> C LOC_Os04g54190.3 downstream_gene_variant ; 29.0bp to feature; MODIFIER N Average:73.287; most accessible tissue: Zhenshan97 root, score: 86.891 N N N N
vg0432278118 G -> C LOC_Os04g54190.2 downstream_gene_variant ; 76.0bp to feature; MODIFIER N Average:73.287; most accessible tissue: Zhenshan97 root, score: 86.891 N N N N
vg0432278118 G -> C LOC_Os04g54180-LOC_Os04g54190 intergenic_region ; MODIFIER N Average:73.287; most accessible tissue: Zhenshan97 root, score: 86.891 N N N N
vg0432278118 G -> DEL N N silent_mutation Average:73.287; most accessible tissue: Zhenshan97 root, score: 86.891 N N N N
vg0432278118 G -> A LOC_Os04g54180.1 upstream_gene_variant ; 1166.0bp to feature; MODIFIER silent_mutation Average:73.287; most accessible tissue: Zhenshan97 root, score: 86.891 N N N N
vg0432278118 G -> A LOC_Os04g54190.1 downstream_gene_variant ; 29.0bp to feature; MODIFIER silent_mutation Average:73.287; most accessible tissue: Zhenshan97 root, score: 86.891 N N N N
vg0432278118 G -> A LOC_Os04g54190.3 downstream_gene_variant ; 29.0bp to feature; MODIFIER silent_mutation Average:73.287; most accessible tissue: Zhenshan97 root, score: 86.891 N N N N
vg0432278118 G -> A LOC_Os04g54190.2 downstream_gene_variant ; 76.0bp to feature; MODIFIER silent_mutation Average:73.287; most accessible tissue: Zhenshan97 root, score: 86.891 N N N N
vg0432278118 G -> A LOC_Os04g54180-LOC_Os04g54190 intergenic_region ; MODIFIER silent_mutation Average:73.287; most accessible tissue: Zhenshan97 root, score: 86.891 N N N N
vg0432278118 G -> T LOC_Os04g54180.1 upstream_gene_variant ; 1166.0bp to feature; MODIFIER N Average:73.287; most accessible tissue: Zhenshan97 root, score: 86.891 N N N N
vg0432278118 G -> T LOC_Os04g54190.1 downstream_gene_variant ; 29.0bp to feature; MODIFIER N Average:73.287; most accessible tissue: Zhenshan97 root, score: 86.891 N N N N
vg0432278118 G -> T LOC_Os04g54190.3 downstream_gene_variant ; 29.0bp to feature; MODIFIER N Average:73.287; most accessible tissue: Zhenshan97 root, score: 86.891 N N N N
vg0432278118 G -> T LOC_Os04g54190.2 downstream_gene_variant ; 76.0bp to feature; MODIFIER N Average:73.287; most accessible tissue: Zhenshan97 root, score: 86.891 N N N N
vg0432278118 G -> T LOC_Os04g54180-LOC_Os04g54190 intergenic_region ; MODIFIER N Average:73.287; most accessible tissue: Zhenshan97 root, score: 86.891 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)
vg0432278118 G A 0.01 0.02 0.02 0.0 -0.01 -0.01
vg0432278118 G C 0.04 0.03 0.02 0.02 0.02 0.02
vg0432278118 G T 0.0 0.01 0.01 0.0 0.01 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0432278118 NA 1.04E-07 mr1559 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
vg0432278118 NA 1.49E-09 mr1794 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
vg0432278118 NA 2.18E-06 mr1041_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
vg0432278118 NA 4.50E-07 mr1043_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
vg0432278118 NA 1.96E-09 mr1084_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
vg0432278118 NA 8.06E-06 mr1185_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
vg0432278118 4.27E-06 8.00E-09 mr1205_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
vg0432278118 NA 2.31E-07 mr1206_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
vg0432278118 3.73E-06 7.74E-08 mr1229_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
vg0432278118 NA 1.19E-06 mr1230_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
vg0432278118 NA 1.46E-06 mr1236_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
vg0432278118 NA 7.33E-07 mr1263_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
vg0432278118 NA 2.35E-06 mr1269_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
vg0432278118 NA 4.20E-07 mr1294_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
vg0432278118 NA 4.85E-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
vg0432278118 NA 1.62E-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
vg0432278118 NA 1.80E-07 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
vg0432278118 NA 6.96E-08 mr1419_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
vg0432278118 NA 1.51E-07 mr1420_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
vg0432278118 NA 1.05E-07 mr1456_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
vg0432278118 NA 2.15E-06 mr1479_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
vg0432278118 NA 2.36E-08 mr1488_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
vg0432278118 NA 9.67E-06 mr1497_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
vg0432278118 NA 3.40E-09 mr1502_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
vg0432278118 NA 3.63E-06 mr1544_2 Jap_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
vg0432278118 NA 1.80E-06 mr1582_2 Jap_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
vg0432278118 3.70E-06 3.99E-07 mr1596_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
vg0432278118 NA 3.68E-08 mr1597_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
vg0432278118 NA 5.47E-08 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
vg0432278118 NA 2.06E-08 mr1668_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
vg0432278118 NA 4.74E-06 mr1677_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
vg0432278118 NA 8.77E-11 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
vg0432278118 NA 3.87E-07 mr1729_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
vg0432278118 NA 7.10E-07 mr1736_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
vg0432278118 NA 1.15E-06 mr1779_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
vg0432278118 NA 1.41E-15 mr1794_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
vg0432278118 NA 4.34E-06 mr1813_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
vg0432278118 NA 9.80E-06 mr1814_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
vg0432278118 NA 8.09E-08 mr1824_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
vg0432278118 8.18E-07 3.73E-09 mr1880_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
vg0432278118 NA 5.95E-08 mr1880_2 Jap_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
vg0432278118 NA 5.10E-06 mr1894_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
vg0432278118 NA 6.17E-08 mr1952_2 Jap_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