Search for Variation information by Variation ID:

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

Detailed information for vg0627961756:

Variant ID: vg0627961756 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 27961756
Reference Allele: CAlternative Allele: A,T
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATTTACACCAGACAAGGTTTTGGCCCAACTTGAGTAGTTGCACACAGGGAAAAATATCATCTGGCCCAAATTCATTGAAATATATTTTTAATAAAAAAAT[C/A,T]
TCTATCCGGCCTGCCGGAATATATTTTCTTTAAAGAGGCCGTGAAGGCCCATACAGGCTCTCCACTAGTAACCACGGCCTTTATCTATCTGGGCCTATTG

Reverse complement sequence

CAATAGGCCCAGATAGATAAAGGCCGTGGTTACTAGTGGAGAGCCTGTATGGGCCTTCACGGCCTCTTTAAAGAAAATATATTCCGGCAGGCCGGATAGA[G/T,A]
ATTTTTTTATTAAAAATATATTTCAATGAATTTGGGCCAGATGATATTTTTCCCTGTGTGCAACTACTCAAGTTGGGCCAAAACCTTGTCTGGTGTAAAT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 93.40% 6.60% 0.00% 0.00% NA
All Indica  2759 88.90% 11.10% 0.00% 0.00% NA
All Japonica  1512 99.70% 0.30% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 93.90% 6.10% 0.00% 0.00% NA
Indica II  465 99.10% 0.90% 0.00% 0.00% NA
Indica III  913 86.70% 13.30% 0.00% 0.00% NA
Indica Intermediate  786 81.60% 18.40% 0.00% 0.00% NA
Temperate Japonica  767 99.30% 0.70% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 98.90% 1.10% 0.00% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0627961756 C -> T LOC_Os06g46140.1 downstream_gene_variant ; 934.0bp to feature; MODIFIER N Average:97.365; most accessible tissue: Zhenshan97 flag leaf, score: 98.62 N N N N
vg0627961756 C -> T LOC_Os06g46149.1 intron_variant ; MODIFIER N Average:97.365; most accessible tissue: Zhenshan97 flag leaf, score: 98.62 N N N N
vg0627961756 C -> T LOC_Os06g46149.2 intron_variant ; MODIFIER N Average:97.365; most accessible tissue: Zhenshan97 flag leaf, score: 98.62 N N N N
vg0627961756 C -> A LOC_Os06g46140.1 downstream_gene_variant ; 934.0bp to feature; MODIFIER silent_mutation Average:97.365; most accessible tissue: Zhenshan97 flag leaf, score: 98.62 N N N N
vg0627961756 C -> A LOC_Os06g46149.1 intron_variant ; MODIFIER silent_mutation Average:97.365; most accessible tissue: Zhenshan97 flag leaf, score: 98.62 N N N N
vg0627961756 C -> A LOC_Os06g46149.2 intron_variant ; MODIFIER silent_mutation Average:97.365; most accessible tissue: Zhenshan97 flag leaf, score: 98.62 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)
vg0627961756 C A -0.11 -0.14 -0.13 -0.11 -0.11 -0.12
vg0627961756 C T -0.14 -0.14 -0.1 -0.11 -0.1 -0.1

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0627961756 NA 7.88E-07 mr1458 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
vg0627961756 NA 4.89E-06 mr1027_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
vg0627961756 NA 7.49E-06 mr1046_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
vg0627961756 NA 6.37E-06 mr1215_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
vg0627961756 NA 2.01E-06 mr1366_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
vg0627961756 NA 3.39E-06 mr1421_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
vg0627961756 NA 1.17E-06 mr1442_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
vg0627961756 NA 3.48E-06 mr1469_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
vg0627961756 NA 1.53E-09 mr1533_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
vg0627961756 NA 8.21E-06 mr1555_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
vg0627961756 NA 1.26E-07 mr1721_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
vg0627961756 NA 3.76E-06 mr1788_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
vg0627961756 NA 4.76E-06 mr1862_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
vg0627961756 NA 2.35E-06 mr1943_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
vg0627961756 NA 2.61E-06 mr1954_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
vg0627961756 4.02E-06 4.02E-06 mr1967_2 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
vg0627961756 NA 5.65E-08 mr1980_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