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Detailed information for vg0318176270:

Variant ID: vg0318176270 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 18176270
Reference Allele: CAlternative Allele: G
Primary Allele: CSecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TATTGTACCCGTTTTTGGCTGAGATGGCGCCTACATAGCTCCTTTTGACCAGGTCTTTGTCCAACGTATCGTTGACGTGGTGCTTATGTAGCAATTAGAT[C/G]
GGAAAAAAATAAAATACGTGGGACCCACATGTTAGTTTCACACACAAATAAGTAAAAAATGGTGGGCCCATGTGGATACTCTCTATCCTCTCTCTCCCTA

Reverse complement sequence

TAGGGAGAGAGAGGATAGAGAGTATCCACATGGGCCCACCATTTTTTACTTATTTGTGTGTGAAACTAACATGTGGGTCCCACGTATTTTATTTTTTTCC[G/C]
ATCTAATTGCTACATAAGCACCACGTCAACGATACGTTGGACAAAGACCTGGTCAAAAGGAGCTATGTAGGCGCCATCTCAGCCAAAAACGGGTACAATA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 32.60% 5.20% 9.42% 52.75% NA
All Indica  2759 3.80% 1.10% 12.03% 83.00% NA
All Japonica  1512 85.80% 0.10% 5.62% 8.47% NA
Aus  269 8.60% 70.30% 9.29% 11.90% NA
Indica I  595 3.40% 0.20% 19.50% 76.97% NA
Indica II  465 4.90% 0.00% 13.33% 81.72% NA
Indica III  913 1.60% 1.40% 5.48% 91.46% NA
Indica Intermediate  786 6.10% 2.20% 13.23% 78.50% NA
Temperate Japonica  767 99.70% 0.00% 0.00% 0.26% NA
Tropical Japonica  504 61.50% 0.20% 16.47% 21.83% NA
Japonica Intermediate  241 92.10% 0.40% 0.83% 6.64% NA
VI/Aromatic  96 75.00% 21.90% 0.00% 3.12% NA
Intermediate  90 48.90% 3.30% 3.33% 44.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0318176270 C -> DEL N N silent_mutation Average:94.379; most accessible tissue: Minghui63 young leaf, score: 98.98 N N N N
vg0318176270 C -> G LOC_Os03g31760.1 upstream_gene_variant ; 4969.0bp to feature; MODIFIER silent_mutation Average:94.379; most accessible tissue: Minghui63 young leaf, score: 98.98 N N N N
vg0318176270 C -> G LOC_Os03g31770.1 upstream_gene_variant ; 882.0bp to feature; MODIFIER silent_mutation Average:94.379; most accessible tissue: Minghui63 young leaf, score: 98.98 N N N N
vg0318176270 C -> G LOC_Os03g31770-LOC_Os03g31790 intergenic_region ; MODIFIER silent_mutation Average:94.379; most accessible tissue: Minghui63 young leaf, score: 98.98 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)
vg0318176270 C G 0.01 0.0 0.0 0.0 0.0 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0318176270 NA 5.89E-07 mr1136 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
vg0318176270 NA 5.23E-11 mr1188 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
vg0318176270 NA 2.60E-09 mr1217 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
vg0318176270 NA 9.03E-07 mr1583 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
vg0318176270 1.69E-06 2.04E-12 mr1718 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
vg0318176270 3.54E-06 NA mr1750 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
vg0318176270 5.87E-11 3.08E-24 mr1750 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
vg0318176270 NA 9.28E-07 mr1785 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
vg0318176270 NA 9.25E-08 mr1845 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
vg0318176270 NA 2.54E-08 mr1852 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
vg0318176270 9.18E-07 9.17E-07 mr1987 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
vg0318176270 NA 6.02E-07 mr1045_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
vg0318176270 NA 7.24E-10 mr1136_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
vg0318176270 NA 2.47E-12 mr1188_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
vg0318176270 NA 6.54E-06 mr1391_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
vg0318176270 6.31E-06 6.30E-06 mr1448_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
vg0318176270 NA 8.61E-12 mr1537_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
vg0318176270 NA 6.12E-14 mr1713_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
vg0318176270 7.44E-06 NA 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
vg0318176270 2.73E-10 8.88E-22 mr1718_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
vg0318176270 1.04E-09 2.45E-33 mr1750_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
vg0318176270 NA 8.71E-08 mr1783_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
vg0318176270 NA 1.03E-07 mr1785_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
vg0318176270 NA 4.87E-09 mr1800_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
vg0318176270 NA 4.30E-08 mr1804_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
vg0318176270 NA 1.96E-13 mr1827_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
vg0318176270 NA 9.49E-08 mr1837_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
vg0318176270 NA 2.54E-11 mr1844_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
vg0318176270 NA 2.60E-09 mr1947_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
vg0318176270 NA 3.89E-07 mr1987_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