Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg1105906564:

Variant ID: vg1105906564 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 5906564
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ACTTCAATTCCTGTCAGAATCCTATGTTTTTCCTATTCCTCCGTTTTTTCTACCCTGCGATTCAAAGGGGCCCTTAGTATGCTAGTGGAGTACTACTGTA[G/A]
TAGTACTAGTCGTCTCCAGCTCACTCGTCCATGATATAACATGGGCTCACTATTCACTAACATGATACTAGTAATGTAGCACATGCATATTTAAAAACAT

Reverse complement sequence

ATGTTTTTAAATATGCATGTGCTACATTACTAGTATCATGTTAGTGAATAGTGAGCCCATGTTATATCATGGACGAGTGAGCTGGAGACGACTAGTACTA[C/T]
TACAGTAGTACTCCACTAGCATACTAAGGGCCCCTTTGAATCGCAGGGTAGAAAAAACGGAGGAATAGGAAAAACATAGGATTCTGACAGGAATTGAAGT

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 87.60% 8.70% 2.45% 1.23% NA
All Indica  2759 80.30% 13.80% 3.91% 1.96% NA
All Japonica  1512 99.50% 0.40% 0.07% 0.07% NA
Aus  269 92.90% 4.80% 1.49% 0.74% NA
Indica I  595 68.10% 20.70% 9.92% 1.34% NA
Indica II  465 96.30% 2.80% 0.86% 0.00% NA
Indica III  913 78.60% 16.50% 1.31% 3.50% NA
Indica Intermediate  786 81.90% 12.10% 4.20% 1.78% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 98.60% 1.00% 0.20% 0.20% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 86.70% 8.90% 3.33% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1105906564 G -> A LOC_Os11g10750.1 upstream_gene_variant ; 3871.0bp to feature; MODIFIER silent_mutation Average:74.722; most accessible tissue: Callus, score: 93.991 N N N N
vg1105906564 G -> A LOC_Os11g10760.1 downstream_gene_variant ; 1386.0bp to feature; MODIFIER silent_mutation Average:74.722; most accessible tissue: Callus, score: 93.991 N N N N
vg1105906564 G -> A LOC_Os11g10750-LOC_Os11g10760 intergenic_region ; MODIFIER silent_mutation Average:74.722; most accessible tissue: Callus, score: 93.991 N N N N
vg1105906564 G -> DEL N N silent_mutation Average:74.722; most accessible tissue: Callus, score: 93.991 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)
vg1105906564 G A -0.13 -0.14 -0.11 -0.19 -0.25 -0.22

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1105906564 1.07E-06 9.45E-11 mr1042 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
vg1105906564 5.83E-06 1.21E-11 mr1042 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
vg1105906564 2.36E-06 2.03E-10 mr1043 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
vg1105906564 NA 5.52E-11 mr1043 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
vg1105906564 2.56E-06 2.69E-09 mr1185 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
vg1105906564 4.50E-06 5.74E-09 mr1185 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
vg1105906564 3.50E-06 6.47E-09 mr1269 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
vg1105906564 3.41E-06 2.36E-08 mr1269 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
vg1105906564 NA 1.26E-09 mr1399 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
vg1105906564 NA 1.64E-07 mr1399 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
vg1105906564 NA 3.54E-08 mr1479 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
vg1105906564 NA 6.07E-08 mr1479 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
vg1105906564 NA 4.59E-06 mr1502 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
vg1105906564 NA 2.28E-06 mr1502 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
vg1105906564 NA 1.67E-08 mr1535 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
vg1105906564 NA 2.51E-06 mr1543 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
vg1105906564 NA 4.77E-08 mr1742 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
vg1105906564 3.82E-06 9.63E-09 mr1912 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
vg1105906564 9.91E-06 2.50E-09 mr1912 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
vg1105906564 NA 2.55E-06 mr1919 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
vg1105906564 NA 1.84E-07 mr1919 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
vg1105906564 NA 3.91E-09 mr1975 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
vg1105906564 NA 3.63E-08 mr1975 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
vg1105906564 NA 2.27E-08 mr1517_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
vg1105906564 NA 7.55E-07 mr1653_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
vg1105906564 NA 7.99E-06 mr1864_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
vg1105906564 NA 6.11E-06 mr1892_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