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Detailed information for vg0106538346:

Variant ID: vg0106538346 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 6538346
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GCCAACACGTGTCCTGTTGTGCAATCTCCGGTTGTCTTTTTTTTGCCTCTCGCATAGTTGCATTGTGACAGCTGACGCGCGCGCGAGAGAGAGAGACAAG[G/A]
TAGAGAGGATTCGTGGGGGATGTGGAGCCATAGAAGTCCAGAAGATGGTCCAATACAACCTAGAACACTTTGAGCGATACCAGCCAACCAGGTGCATAGT

Reverse complement sequence

ACTATGCACCTGGTTGGCTGGTATCGCTCAAAGTGTTCTAGGTTGTATTGGACCATCTTCTGGACTTCTATGGCTCCACATCCCCCACGAATCCTCTCTA[C/T]
CTTGTCTCTCTCTCTCGCGCGCGCGTCAGCTGTCACAATGCAACTATGCGAGAGGCAAAAAAAAGACAACCGGAGATTGCACAACAGGACACGTGTTGGC

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 58.40% 41.40% 0.15% 0.00% NA
All Indica  2759 87.90% 11.90% 0.22% 0.00% NA
All Japonica  1512 18.70% 81.30% 0.00% 0.00% NA
Aus  269 0.40% 99.60% 0.00% 0.00% NA
Indica I  595 97.10% 2.90% 0.00% 0.00% NA
Indica II  465 74.20% 24.90% 0.86% 0.00% NA
Indica III  913 93.50% 6.50% 0.00% 0.00% NA
Indica Intermediate  786 82.60% 17.20% 0.25% 0.00% NA
Temperate Japonica  767 2.70% 97.30% 0.00% 0.00% NA
Tropical Japonica  504 29.80% 70.20% 0.00% 0.00% NA
Japonica Intermediate  241 46.50% 53.50% 0.00% 0.00% NA
VI/Aromatic  96 5.20% 94.80% 0.00% 0.00% NA
Intermediate  90 51.10% 47.80% 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
vg0106538346 G -> A LOC_Os01g12010.1 upstream_gene_variant ; 450.0bp to feature; MODIFIER silent_mutation Average:88.73; most accessible tissue: Zhenshan97 flower, score: 96.658 N N N N
vg0106538346 G -> A LOC_Os01g12020.1 upstream_gene_variant ; 2659.0bp to feature; MODIFIER silent_mutation Average:88.73; most accessible tissue: Zhenshan97 flower, score: 96.658 N N N N
vg0106538346 G -> A LOC_Os01g12000.1 downstream_gene_variant ; 2509.0bp to feature; MODIFIER silent_mutation Average:88.73; most accessible tissue: Zhenshan97 flower, score: 96.658 N N N N
vg0106538346 G -> A LOC_Os01g12030.1 downstream_gene_variant ; 3625.0bp to feature; MODIFIER silent_mutation Average:88.73; most accessible tissue: Zhenshan97 flower, score: 96.658 N N N N
vg0106538346 G -> A LOC_Os01g12010-LOC_Os01g12020 intergenic_region ; MODIFIER silent_mutation Average:88.73; most accessible tissue: Zhenshan97 flower, score: 96.658 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)
vg0106538346 G A -0.06 0.02 0.04 -0.11 -0.07 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0106538346 NA 1.32E-07 mr1188 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
vg0106538346 5.90E-08 3.09E-07 mr1498 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
vg0106538346 2.77E-12 2.48E-27 mr1498 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
vg0106538346 NA 2.29E-21 mr1598 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
vg0106538346 2.50E-08 NA mr1769 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
vg0106538346 1.10E-13 3.88E-31 mr1769 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
vg0106538346 NA 2.96E-07 mr1881 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
vg0106538346 4.10E-07 2.03E-12 mr1925 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
vg0106538346 NA 8.07E-22 mr1943 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
vg0106538346 1.09E-06 NA mr1951 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
vg0106538346 3.15E-13 1.42E-23 mr1951 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
vg0106538346 NA 1.03E-09 mr1188_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
vg0106538346 NA 1.71E-37 mr1208_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
vg0106538346 NA 8.03E-10 mr1310_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
vg0106538346 NA 3.16E-16 mr1457_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
vg0106538346 4.55E-07 NA mr1498_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
vg0106538346 1.39E-08 5.69E-21 mr1498_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
vg0106538346 1.88E-06 NA mr1769_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
vg0106538346 1.05E-12 4.40E-32 mr1769_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
vg0106538346 4.86E-06 NA mr1916_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
vg0106538346 5.16E-09 4.24E-11 mr1916_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
vg0106538346 7.51E-06 2.72E-10 mr1925_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
vg0106538346 1.45E-06 2.21E-14 mr1951_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