Search for Variation information by Variation ID:

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

Detailed information for vg0141707795:

Variant ID: vg0141707795 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 41707795
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.84, G: 0.14, others allele: 0.00, population size: 76. )

Flanking Sequence (100 bp) in Reference Genome:


GCCAACTGGAAGGAAGGAATTACTCCCTAGGTTTTTTTTTAAGTACTCCCTCCGTCCTTAAAAAATAAAAAAAGACAAACCCTAGATTTTTGTGTCCAAC[A/G]
TTTGACTATCCGTCTTATATAAATTTTTTTATAATTAGTATTTTCATTGTTGTTAGATGATAAAACATGATTAATATTTTATGCGTGACTTATCTTTTTA

Reverse complement sequence

TAAAAAGATAAGTCACGCATAAAATATTAATCATGTTTTATCATCTAACAACAATGAAAATACTAATTATAAAAAAATTTATATAAGACGGATAGTCAAA[T/C]
GTTGGACACAAAAATCTAGGGTTTGTCTTTTTTTATTTTTTAAGGACGGAGGGAGTACTTAAAAAAAAACCTAGGGAGTAATTCCTTCCTTCCAGTTGGC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 59.40% 39.10% 0.47% 0.95% NA
All Indica  2759 85.10% 12.60% 0.76% 1.52% NA
All Japonica  1512 4.80% 95.10% 0.00% 0.07% NA
Aus  269 98.50% 1.50% 0.00% 0.00% NA
Indica I  595 77.10% 21.70% 1.18% 0.00% NA
Indica II  465 82.20% 10.50% 1.08% 6.24% NA
Indica III  913 98.20% 1.00% 0.33% 0.44% NA
Indica Intermediate  786 77.70% 20.40% 0.76% 1.15% NA
Temperate Japonica  767 0.90% 99.10% 0.00% 0.00% NA
Tropical Japonica  504 9.90% 90.10% 0.00% 0.00% NA
Japonica Intermediate  241 6.60% 92.90% 0.00% 0.41% NA
VI/Aromatic  96 82.30% 17.70% 0.00% 0.00% NA
Intermediate  90 47.80% 48.90% 1.11% 2.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0141707795 A -> G LOC_Os01g71970.1 upstream_gene_variant ; 4086.0bp to feature; MODIFIER silent_mutation Average:68.044; most accessible tissue: Zhenshan97 flower, score: 91.056 N N N N
vg0141707795 A -> G LOC_Os01g71960-LOC_Os01g71970 intergenic_region ; MODIFIER silent_mutation Average:68.044; most accessible tissue: Zhenshan97 flower, score: 91.056 N N N N
vg0141707795 A -> DEL N N silent_mutation Average:68.044; most accessible tissue: Zhenshan97 flower, score: 91.056 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)
vg0141707795 A G 0.01 0.0 0.0 0.01 0.0 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0141707795 NA 1.76E-06 Spikelet_length Ind_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
vg0141707795 NA 6.26E-12 mr1322 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
vg0141707795 NA 7.59E-12 mr1325 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
vg0141707795 NA 8.11E-14 mr1326 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
vg0141707795 NA 1.98E-06 mr1389 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
vg0141707795 NA 4.81E-07 mr1527 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
vg0141707795 NA 7.44E-08 mr1532 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
vg0141707795 NA 9.86E-12 mr1553 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
vg0141707795 NA 8.11E-07 mr1690 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
vg0141707795 NA 4.42E-09 mr1038_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
vg0141707795 NA 5.85E-08 mr1170_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
vg0141707795 NA 2.45E-06 mr1389_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
vg0141707795 NA 8.24E-06 mr1480_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
vg0141707795 NA 2.10E-12 mr1553_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
vg0141707795 NA 1.28E-10 mr1749_2 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
vg0141707795 NA 2.86E-06 mr1785_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
vg0141707795 NA 1.36E-09 mr1821_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
vg0141707795 NA 2.90E-09 mr1968_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
vg0141707795 NA 3.76E-08 mr1974_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