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Detailed information for vg1126981238:

Variant ID: vg1126981238 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 26981238
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.84, G: 0.16, others allele: 0.00, population size: 92. )

Flanking Sequence (100 bp) in Reference Genome:


TTCGTCAAAAAAATTGATCTGATGTACTAGTGATCGGGCATTCACCGTTATAAATTACTCCTCGCCTCAAACCACCGAGGTGGTACTAAACTTTGCCACA[A/G]
TATACTTCTGCTGCTGGCTGTTGCCGATCTGCTGCTGCTCGCGAAATGGGCCAAGGCCCAATGCCCGCTGCTGCACCACTACTGCTCCTGCTGCTGCAAT

Reverse complement sequence

ATTGCAGCAGCAGGAGCAGTAGTGGTGCAGCAGCGGGCATTGGGCCTTGGCCCATTTCGCGAGCAGCAGCAGATCGGCAACAGCCAGCAGCAGAAGTATA[T/C]
TGTGGCAAAGTTTAGTACCACCTCGGTGGTTTGAGGCGAGGAGTAATTTATAACGGTGAATGCCCGATCACTAGTACATCAGATCAATTTTTTTGACGAA

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 75.50% 22.20% 0.36% 1.97% NA
All Indica  2759 64.30% 32.40% 0.47% 2.90% NA
All Japonica  1512 94.00% 5.40% 0.13% 0.46% NA
Aus  269 79.60% 17.80% 0.74% 1.86% NA
Indica I  595 60.70% 38.30% 0.17% 0.84% NA
Indica II  465 41.90% 58.10% 0.00% 0.00% NA
Indica III  913 77.40% 17.90% 0.66% 4.05% NA
Indica Intermediate  786 64.90% 29.50% 0.76% 4.83% NA
Temperate Japonica  767 93.60% 6.00% 0.26% 0.13% NA
Tropical Japonica  504 97.20% 2.20% 0.00% 0.60% NA
Japonica Intermediate  241 88.80% 10.00% 0.00% 1.24% NA
VI/Aromatic  96 89.60% 10.40% 0.00% 0.00% NA
Intermediate  90 78.90% 20.00% 0.00% 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
vg1126981238 A -> DEL N N silent_mutation Average:91.777; most accessible tissue: Callus, score: 98.559 N N N N
vg1126981238 A -> G LOC_Os11g44600.1 downstream_gene_variant ; 3449.0bp to feature; MODIFIER silent_mutation Average:91.777; most accessible tissue: Callus, score: 98.559 N N N N
vg1126981238 A -> G LOC_Os11g44630.1 downstream_gene_variant ; 1868.0bp to feature; MODIFIER silent_mutation Average:91.777; most accessible tissue: Callus, score: 98.559 N N N N
vg1126981238 A -> G LOC_Os11g44600-LOC_Os11g44630 intergenic_region ; MODIFIER silent_mutation Average:91.777; most accessible tissue: Callus, score: 98.559 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)
vg1126981238 A G 0.07 0.09 0.07 0.09 0.06 0.06

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1126981238 NA 1.41E-07 mr1122 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
vg1126981238 NA 2.41E-09 mr1133 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
vg1126981238 NA 3.84E-06 mr1181 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
vg1126981238 2.07E-06 2.07E-06 mr1299 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
vg1126981238 3.40E-06 6.34E-08 mr1376 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
vg1126981238 3.40E-06 6.34E-08 mr1431 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
vg1126981238 5.54E-06 5.54E-06 mr1576 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
vg1126981238 NA 5.83E-06 mr1696 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
vg1126981238 NA 1.19E-07 mr1756 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
vg1126981238 5.75E-06 5.75E-06 mr1756 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
vg1126981238 NA 4.20E-06 mr1775 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
vg1126981238 NA 7.40E-07 mr1133_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
vg1126981238 1.18E-09 1.18E-09 mr1191_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
vg1126981238 NA 1.05E-06 mr1380_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
vg1126981238 NA 5.88E-08 mr1561_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
vg1126981238 NA 1.36E-06 mr1875_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
vg1126981238 NA 1.65E-07 mr1908_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
vg1126981238 NA 1.34E-06 mr1996_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