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Detailed information for vg1120893049:

Variant ID: vg1120893049 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 20893049
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ACACCTAGCACTGCAGCCCTGCTCCCTCCGTCACACCGGCCGCGCTGCAGCAGCCGTCGCCGTCGCTCCGCCTCAGCAGTCGACGGGTGCAGCACTCCTC[C/T]
GCTCACAGCGCCGCCGCCACACGTCCTCCCCAACACCAGCGTCTCCCTCCTCGACGAGCTCTGGCGAGGCTAGGGTTTAGCCGTCGCCAGCCACTAGCCG

Reverse complement sequence

CGGCTAGTGGCTGGCGACGGCTAAACCCTAGCCTCGCCAGAGCTCGTCGAGGAGGGAGACGCTGGTGTTGGGGAGGACGTGTGGCGGCGGCGCTGTGAGC[G/A]
GAGGAGTGCTGCACCCGTCGACTGCTGAGGCGGAGCGACGGCGACGGCTGCTGCAGCGCGGCCGGTGTGACGGAGGGAGCAGGGCTGCAGTGCTAGGTGT

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 53.30% 16.80% 1.76% 28.14% NA
All Indica  2759 52.00% 1.20% 1.52% 45.23% NA
All Japonica  1512 51.50% 43.80% 2.12% 2.58% NA
Aus  269 88.80% 0.40% 1.12% 9.67% NA
Indica I  595 83.70% 1.50% 1.01% 13.78% NA
Indica II  465 68.60% 0.90% 0.22% 30.32% NA
Indica III  913 20.30% 0.70% 2.85% 76.23% NA
Indica Intermediate  786 55.10% 1.90% 1.15% 41.86% NA
Temperate Japonica  767 78.40% 18.30% 2.48% 0.91% NA
Tropical Japonica  504 18.70% 74.60% 1.19% 5.56% NA
Japonica Intermediate  241 34.40% 61.00% 2.90% 1.66% NA
VI/Aromatic  96 18.80% 77.10% 0.00% 4.17% NA
Intermediate  90 54.40% 24.40% 6.67% 14.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1120893049 C -> T LOC_Os11g35630.1 upstream_gene_variant ; 1033.0bp to feature; MODIFIER silent_mutation Average:47.137; most accessible tissue: Zhenshan97 panicle, score: 92.133 N N N N
vg1120893049 C -> T LOC_Os11g35630-LOC_Os11g35650 intergenic_region ; MODIFIER silent_mutation Average:47.137; most accessible tissue: Zhenshan97 panicle, score: 92.133 N N N N
vg1120893049 C -> DEL N N silent_mutation Average:47.137; most accessible tissue: Zhenshan97 panicle, score: 92.133 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)
vg1120893049 C T 0.01 0.02 0.02 -0.01 0.0 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1120893049 NA 1.56E-06 mr1031 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
vg1120893049 NA 3.52E-06 mr1056 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
vg1120893049 NA 2.99E-14 mr1084 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
vg1120893049 NA 3.07E-14 mr1205 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
vg1120893049 NA 2.04E-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
vg1120893049 NA 9.76E-09 mr1332 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
vg1120893049 NA 3.18E-12 mr1454 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
vg1120893049 NA 8.85E-15 mr1521 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
vg1120893049 NA 1.30E-06 mr1596 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
vg1120893049 NA 8.98E-08 mr1668 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
vg1120893049 NA 1.94E-06 mr1729 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
vg1120893049 NA 6.74E-06 mr1763 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
vg1120893049 NA 1.06E-14 mr1775 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
vg1120893049 NA 6.03E-07 mr1810 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
vg1120893049 NA 1.31E-06 mr1979 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
vg1120893049 4.23E-06 4.23E-06 mr1181_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
vg1120893049 NA 6.29E-09 mr1851_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
vg1120893049 NA 8.25E-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