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Detailed information for vg1122081867:

Variant ID: vg1122081867 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 22081867
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.85, T: 0.14, others allele: 0.00, population size: 69. )

Flanking Sequence (100 bp) in Reference Genome:


AGTCCCACCTCGCTCACCGAATGAACATTGCACTAACTTATAAACCGAGGCATGGATGCTGCCGACGAGAAACACTGGAACTTGAGCTGGGCAGATCGTG[C/T]
AATATTCGTTATCGGATTTGCACGAAACCATATATTGTTTAGGTATAACTTGTTCATTCTGGGCCTTGGATTTCAGCGACTACGGCGAGTTCACCCCTAC

Reverse complement sequence

GTAGGGGTGAACTCGCCGTAGTCGCTGAAATCCAAGGCCCAGAATGAACAAGTTATACCTAAACAATATATGGTTTCGTGCAAATCCGATAACGAATATT[G/A]
CACGATCTGCCCAGCTCAAGTTCCAGTGTTTCTCGTCGGCAGCATCCATGCCTCGGTTTATAAGTTAGTGCAATGTTCATTCGGTGAGCGAGGTGGGACT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 25.50% 22.00% 0.85% 51.57% NA
All Indica  2759 3.80% 28.60% 0.65% 66.94% NA
All Japonica  1512 65.80% 3.20% 1.39% 29.56% NA
Aus  269 4.10% 65.40% 0.00% 30.48% NA
Indica I  595 2.70% 30.80% 0.67% 65.88% NA
Indica II  465 0.90% 34.80% 0.43% 63.87% NA
Indica III  913 6.60% 21.50% 0.33% 71.63% NA
Indica Intermediate  786 3.30% 31.40% 1.15% 64.12% NA
Temperate Japonica  767 84.10% 4.60% 0.65% 10.69% NA
Tropical Japonica  504 48.40% 1.60% 2.18% 47.82% NA
Japonica Intermediate  241 44.00% 2.50% 2.07% 51.45% NA
VI/Aromatic  96 64.60% 10.40% 1.04% 23.96% NA
Intermediate  90 36.70% 21.10% 0.00% 42.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1122081867 C -> T LOC_Os11g37400.1 upstream_gene_variant ; 3173.0bp to feature; MODIFIER silent_mutation Average:56.232; most accessible tissue: Zhenshan97 root, score: 98.823 N N N N
vg1122081867 C -> T LOC_Os11g37390-LOC_Os11g37400 intergenic_region ; MODIFIER silent_mutation Average:56.232; most accessible tissue: Zhenshan97 root, score: 98.823 N N N N
vg1122081867 C -> DEL N N silent_mutation Average:56.232; most accessible tissue: Zhenshan97 root, score: 98.823 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)
vg1122081867 C T -0.03 -0.03 -0.02 -0.02 -0.02 -0.03

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1122081867 NA 6.56E-06 mr1106 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
vg1122081867 NA 6.96E-11 mr1128 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
vg1122081867 NA 2.98E-07 mr1190 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
vg1122081867 NA 8.50E-09 mr1302 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
vg1122081867 NA 1.48E-06 mr1315 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
vg1122081867 NA 3.66E-14 mr1376 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
vg1122081867 NA 8.86E-06 mr1418 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
vg1122081867 NA 6.17E-07 mr1420 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
vg1122081867 NA 3.66E-14 mr1431 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
vg1122081867 NA 3.49E-07 mr1659 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
vg1122081867 NA 1.18E-09 mr1776 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
vg1122081867 NA 2.34E-07 mr1797 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
vg1122081867 NA 2.34E-07 mr1801 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
vg1122081867 NA 1.41E-06 mr1886 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
vg1122081867 NA 3.22E-09 mr1986 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
vg1122081867 NA 8.72E-07 mr1517_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
vg1122081867 8.66E-06 2.20E-06 mr1561_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
vg1122081867 5.27E-06 7.66E-06 mr1875_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
vg1122081867 4.76E-06 4.76E-06 mr1908_2 Jap_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