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Detailed information for vg1123155726:

Variant ID: vg1123155726 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 23155726
Reference Allele: TAlternative Allele: G,A
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.62, T: 0.38, others allele: 0.00, population size: 81. )

Flanking Sequence (100 bp) in Reference Genome:


AAAATGTGAGTGGAGGAGGCGGGCGTTTATTTGGAAAAGTGCTACGCTTGTGATTTGGCCCCAGGATCTTGATCGAATGGCTATGAACTCTCGTGTGCAT[T/G,A]
AGTGCAGCTACATATCTGTGTATAGGATACATTATATATATATATATATATATATATATATATATATGGGAGCGTATTCTATGCACACAGGCCCTCGCGT

Reverse complement sequence

ACGCGAGGGCCTGTGTGCATAGAATACGCTCCCATATATATATATATATATATATATATATATATATAATGTATCCTATACACAGATATGTAGCTGCACT[A/C,T]
ATGCACACGAGAGTTCATAGCCATTCGATCAAGATCCTGGGGCCAAATCACAAGCGTAGCACTTTTCCAAATAAACGCCCGCCTCCTCCACTCACATTTT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 30.60% 19.40% 3.75% 46.00% A: 0.23%
All Indica  2759 23.20% 9.10% 2.83% 64.52% A: 0.40%
All Japonica  1512 42.70% 39.00% 1.65% 16.67% NA
Aus  269 42.80% 22.30% 1.49% 33.46% NA
Indica I  595 49.40% 4.50% 1.51% 44.54% NA
Indica II  465 7.30% 3.00% 1.29% 88.39% NA
Indica III  913 21.20% 12.70% 3.72% 61.12% A: 1.20%
Indica Intermediate  786 15.00% 11.80% 3.69% 69.47% NA
Temperate Japonica  767 15.60% 70.90% 0.52% 12.91% NA
Tropical Japonica  504 75.40% 4.40% 3.17% 17.06% NA
Japonica Intermediate  241 60.20% 10.00% 2.07% 27.80% NA
VI/Aromatic  96 21.90% 5.20% 63.54% 9.38% NA
Intermediate  90 27.80% 14.40% 10.00% 47.78% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1123155726 T -> DEL N N silent_mutation Average:90.212; most accessible tissue: Callus, score: 98.307 N N N N
vg1123155726 T -> A LOC_Os11g38900.1 upstream_gene_variant ; 2746.0bp to feature; MODIFIER silent_mutation Average:90.212; most accessible tissue: Callus, score: 98.307 N N N N
vg1123155726 T -> A LOC_Os11g38890.1 downstream_gene_variant ; 1070.0bp to feature; MODIFIER silent_mutation Average:90.212; most accessible tissue: Callus, score: 98.307 N N N N
vg1123155726 T -> A LOC_Os11g38890-LOC_Os11g38900 intergenic_region ; MODIFIER silent_mutation Average:90.212; most accessible tissue: Callus, score: 98.307 N N N N
vg1123155726 T -> G LOC_Os11g38900.1 upstream_gene_variant ; 2746.0bp to feature; MODIFIER silent_mutation Average:90.212; most accessible tissue: Callus, score: 98.307 N N N N
vg1123155726 T -> G LOC_Os11g38890.1 downstream_gene_variant ; 1070.0bp to feature; MODIFIER silent_mutation Average:90.212; most accessible tissue: Callus, score: 98.307 N N N N
vg1123155726 T -> G LOC_Os11g38890-LOC_Os11g38900 intergenic_region ; MODIFIER silent_mutation Average:90.212; most accessible tissue: Callus, score: 98.307 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)
vg1123155726 T A -0.01 -0.01 -0.01 0.0 -0.01 -0.01
vg1123155726 T G -0.01 -0.01 -0.01 -0.01 -0.01 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1123155726 NA 3.13E-12 Spikelet_length Jap_All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg1123155726 NA 2.36E-06 mr1030 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
vg1123155726 NA 2.14E-08 mr1045 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
vg1123155726 NA 1.18E-10 mr1137 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
vg1123155726 NA 2.27E-06 mr1192 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
vg1123155726 NA 3.40E-07 mr1229 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
vg1123155726 NA 7.69E-07 mr1252 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
vg1123155726 NA 5.31E-08 mr1318 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
vg1123155726 NA 2.81E-06 mr1359 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
vg1123155726 NA 6.12E-07 mr1378 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
vg1123155726 NA 1.57E-09 mr1486 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
vg1123155726 NA 9.52E-06 mr1520 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
vg1123155726 NA 6.16E-06 mr1576 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
vg1123155726 NA 1.67E-07 mr1579 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
vg1123155726 NA 1.16E-22 mr1611 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
vg1123155726 NA 1.22E-13 mr1611 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
vg1123155726 NA 2.36E-06 mr1614 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
vg1123155726 NA 8.32E-10 mr1617 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
vg1123155726 NA 8.78E-06 mr1621 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
vg1123155726 NA 2.01E-06 mr1627 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
vg1123155726 NA 1.52E-07 mr1729 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
vg1123155726 NA 1.17E-12 mr1741 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
vg1123155726 NA 2.67E-07 mr1763 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
vg1123155726 NA 2.08E-07 mr1804 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
vg1123155726 NA 8.54E-06 mr1826 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
vg1123155726 NA 1.82E-07 mr1880 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
vg1123155726 NA 6.72E-08 mr1137_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
vg1123155726 NA 6.48E-06 mr1263_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
vg1123155726 NA 9.76E-07 mr1617_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
vg1123155726 NA 9.20E-06 mr1672_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
vg1123155726 NA 1.16E-07 mr1693_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
vg1123155726 NA 4.82E-07 mr1880_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