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Detailed information for vg1109260557:

Variant ID: vg1109260557 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 9260557
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 101. )

Flanking Sequence (100 bp) in Reference Genome:


CCCAAGAAATCCCCAAAAGTTTCTACGGAAATCCTTTCCAATTTCGCGGTTCAATTTTTCCTTTTTCCGGCGAGAACCCTAGATTTTCCCGAGTTTTTCC[C/T]
GTCGATGTGGGCTTGATCCCGAGCTCCCGTGCCTATATAAAGGACCCCCTCGTCGTACTCTACCTATCCCCTCAAGTCCCGTCCTCCACCGTCGCCGCAA

Reverse complement sequence

TTGCGGCGACGGTGGAGGACGGGACTTGAGGGGATAGGTAGAGTACGACGAGGGGGTCCTTTATATAGGCACGGGAGCTCGGGATCAAGCCCACATCGAC[G/A]
GGAAAAACTCGGGAAAATCTAGGGTTCTCGCCGGAAAAAGGAAAAATTGAACCGCGAAATTGGAAAGGATTTCCGTAGAAACTTTTGGGGATTTCTTGGG

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 49.80% 14.10% 0.63% 35.44% NA
All Indica  2759 17.00% 23.30% 1.01% 58.68% NA
All Japonica  1512 97.60% 0.10% 0.07% 2.25% NA
Aus  269 98.10% 1.10% 0.37% 0.37% NA
Indica I  595 23.00% 0.80% 1.01% 75.13% NA
Indica II  465 6.20% 56.30% 0.65% 36.77% NA
Indica III  913 12.90% 24.10% 0.99% 61.99% NA
Indica Intermediate  786 23.40% 20.00% 1.27% 55.34% NA
Temperate Japonica  767 97.40% 0.00% 0.00% 2.61% NA
Tropical Japonica  504 97.20% 0.40% 0.20% 2.18% NA
Japonica Intermediate  241 98.80% 0.00% 0.00% 1.24% NA
VI/Aromatic  96 99.00% 0.00% 0.00% 1.04% NA
Intermediate  90 58.90% 18.90% 0.00% 22.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1109260557 C -> T LOC_Os11g16690.1 upstream_gene_variant ; 3499.0bp to feature; MODIFIER silent_mutation Average:56.204; most accessible tissue: Minghui63 flag leaf, score: 90.512 N N N N
vg1109260557 C -> T LOC_Os11g16720.1 upstream_gene_variant ; 3780.0bp to feature; MODIFIER silent_mutation Average:56.204; most accessible tissue: Minghui63 flag leaf, score: 90.512 N N N N
vg1109260557 C -> T LOC_Os11g16710.1 downstream_gene_variant ; 64.0bp to feature; MODIFIER silent_mutation Average:56.204; most accessible tissue: Minghui63 flag leaf, score: 90.512 N N N N
vg1109260557 C -> T LOC_Os11g16690-LOC_Os11g16710 intergenic_region ; MODIFIER silent_mutation Average:56.204; most accessible tissue: Minghui63 flag leaf, score: 90.512 N N N N
vg1109260557 C -> DEL N N silent_mutation Average:56.204; most accessible tissue: Minghui63 flag leaf, score: 90.512 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)
vg1109260557 C T -0.01 -0.01 -0.03 -0.01 -0.02 -0.04

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1109260557 NA 4.76E-06 mr1352 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
vg1109260557 NA 2.63E-07 mr1609 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
vg1109260557 NA 6.80E-06 mr1805 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
vg1109260557 NA 8.66E-06 mr1806 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
vg1109260557 NA 1.48E-07 mr1829 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
vg1109260557 NA 1.25E-10 mr1829 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
vg1109260557 NA 7.40E-07 mr1842 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
vg1109260557 NA 1.77E-09 mr1902 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
vg1109260557 NA 2.38E-10 mr1829_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
vg1109260557 NA 1.29E-06 mr1842_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
vg1109260557 NA 3.78E-09 mr1902_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
vg1109260557 NA 8.16E-07 mr1933_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