Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg1117177295:

Variant ID: vg1117177295 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 17177295
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.67, A: 0.32, others allele: 0.00, population size: 72. )

Flanking Sequence (100 bp) in Reference Genome:


TAAACTTGTAACGTCAGCGAAACTGGCCATGCATACTACTGATTTAAACCGGTTTAGGGTGTGTTTAGTTCACGTCAAAATTAAAAGTTTGGTTGAAATT[G/A]
AAACAATGTGACGAAAAAATTGGAAGTTCATGTGTGTAGAAAAGTTTTGATGTAATAGAAAAGTTGAAAGTTTGAAGAAAAAATTTGGAACTAAACAAGG

Reverse complement sequence

CCTTGTTTAGTTCCAAATTTTTTCTTCAAACTTTCAACTTTTCTATTACATCAAAACTTTTCTACACACATGAACTTCCAATTTTTTCGTCACATTGTTT[C/T]
AATTTCAACCAAACTTTTAATTTTGACGTGAACTAAACACACCCTAAACCGGTTTAAATCAGTAGTATGCATGGCCAGTTTCGCTGACGTTACAAGTTTA

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 41.80% 39.90% 0.61% 17.69% NA
All Indica  2759 35.60% 40.10% 0.87% 23.49% NA
All Japonica  1512 53.80% 45.40% 0.00% 0.79% NA
Aus  269 14.10% 23.40% 1.86% 60.59% NA
Indica I  595 35.10% 63.70% 0.17% 1.01% NA
Indica II  465 31.80% 15.70% 1.51% 50.97% NA
Indica III  913 39.00% 38.60% 0.22% 22.23% NA
Indica Intermediate  786 34.10% 38.40% 1.78% 25.70% NA
Temperate Japonica  767 16.00% 83.20% 0.00% 0.78% NA
Tropical Japonica  504 96.80% 2.20% 0.00% 0.99% NA
Japonica Intermediate  241 83.80% 15.80% 0.00% 0.41% NA
VI/Aromatic  96 93.80% 3.10% 0.00% 3.12% NA
Intermediate  90 57.80% 31.10% 0.00% 11.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1117177295 G -> A LOC_Os11g29610.1 downstream_gene_variant ; 2105.0bp to feature; MODIFIER silent_mutation Average:81.012; most accessible tissue: Callus, score: 92.562 N N N N
vg1117177295 G -> A LOC_Os11g29620.1 downstream_gene_variant ; 2055.0bp to feature; MODIFIER silent_mutation Average:81.012; most accessible tissue: Callus, score: 92.562 N N N N
vg1117177295 G -> A LOC_Os11g29630.1 downstream_gene_variant ; 3234.0bp to feature; MODIFIER silent_mutation Average:81.012; most accessible tissue: Callus, score: 92.562 N N N N
vg1117177295 G -> A LOC_Os11g29610-LOC_Os11g29620 intergenic_region ; MODIFIER silent_mutation Average:81.012; most accessible tissue: Callus, score: 92.562 N N N N
vg1117177295 G -> DEL N N silent_mutation Average:81.012; most accessible tissue: Callus, score: 92.562 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)
vg1117177295 G A 0.02 0.01 0.01 0.02 0.0 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1117177295 NA 2.56E-14 Grain_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
vg1117177295 NA 8.12E-06 mr1048 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
vg1117177295 NA 1.98E-07 mr1170 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
vg1117177295 NA 8.84E-07 mr1184 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
vg1117177295 NA 2.67E-08 mr1206 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
vg1117177295 NA 2.05E-09 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
vg1117177295 6.64E-06 6.64E-06 mr1230 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
vg1117177295 NA 9.43E-08 mr1319 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
vg1117177295 NA 6.04E-06 mr1336 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
vg1117177295 NA 1.06E-06 mr1380 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
vg1117177295 2.50E-06 2.50E-06 mr1391 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
vg1117177295 NA 6.17E-06 mr1438 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
vg1117177295 NA 1.95E-06 mr1530 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
vg1117177295 NA 2.44E-06 mr1550 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
vg1117177295 NA 4.98E-06 mr1579 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
vg1117177295 NA 8.23E-07 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
vg1117177295 NA 1.86E-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
vg1117177295 NA 1.34E-07 mr1739 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
vg1117177295 NA 1.29E-07 mr1739 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
vg1117177295 NA 8.42E-07 mr1740 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
vg1117177295 NA 1.02E-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
vg1117177295 NA 4.56E-07 mr1863 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
vg1117177295 NA 2.33E-06 mr1906 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
vg1117177295 NA 7.79E-06 mr1906 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
vg1117177295 NA 9.69E-06 mr1170_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
vg1117177295 NA 6.17E-06 mr1236_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