Search for Variation information by Variation ID:

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

Detailed information for vg0140493557:

Variant ID: vg0140493557 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 40493557
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, C: 0.01, others allele: 0.00, population size: 116. )

Flanking Sequence (100 bp) in Reference Genome:


ACTATGACATATGGGTCCAGTAGCAAATCCTTTATCACCACTCGTAAGAGTGGCAAATAGTTAATTATCCCGGTCTAAAATACATGTTTTGAACTTGGGG[T/C]
GTATGTTTTACACCAAGGGAAAGACTAGTGGGGAGGTAAAGTGGACTTATCCCAAATTGGAATTCCTTTTCTAATGTGATGTTAGGCTGGACCGGGATGG

Reverse complement sequence

CCATCCCGGTCCAGCCTAACATCACATTAGAAAAGGAATTCCAATTTGGGATAAGTCCACTTTACCTCCCCACTAGTCTTTCCCTTGGTGTAAAACATAC[A/G]
CCCCAAGTTCAAAACATGTATTTTAGACCGGGATAATTAACTATTTGCCACTCTTACGAGTGGTGATAAAGGATTTGCTACTGGACCCATATGTCATAGT

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 54.10% 45.70% 0.15% 0.00% NA
All Indica  2759 77.90% 21.90% 0.22% 0.00% NA
All Japonica  1512 2.20% 97.80% 0.00% 0.00% NA
Aus  269 92.60% 7.40% 0.00% 0.00% NA
Indica I  595 69.10% 30.60% 0.34% 0.00% NA
Indica II  465 89.20% 10.80% 0.00% 0.00% NA
Indica III  913 82.50% 17.30% 0.22% 0.00% NA
Indica Intermediate  786 72.50% 27.20% 0.25% 0.00% NA
Temperate Japonica  767 0.30% 99.70% 0.00% 0.00% NA
Tropical Japonica  504 4.20% 95.80% 0.00% 0.00% NA
Japonica Intermediate  241 4.60% 95.40% 0.00% 0.00% NA
VI/Aromatic  96 92.70% 7.30% 0.00% 0.00% NA
Intermediate  90 42.20% 56.70% 1.11% 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
vg0140493557 T -> C LOC_Os01g69990.1 upstream_gene_variant ; 3897.0bp to feature; MODIFIER silent_mutation Average:96.108; most accessible tissue: Zhenshan97 flag leaf, score: 97.754 N N N N
vg0140493557 T -> C LOC_Os01g70000.1 upstream_gene_variant ; 137.0bp to feature; MODIFIER silent_mutation Average:96.108; most accessible tissue: Zhenshan97 flag leaf, score: 97.754 N N N N
vg0140493557 T -> C LOC_Os01g70010.1 downstream_gene_variant ; 2786.0bp to feature; MODIFIER silent_mutation Average:96.108; most accessible tissue: Zhenshan97 flag leaf, score: 97.754 N N N N
vg0140493557 T -> C LOC_Os01g69990-LOC_Os01g70000 intergenic_region ; MODIFIER silent_mutation Average:96.108; most accessible tissue: Zhenshan97 flag leaf, score: 97.754 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)
vg0140493557 T C 0.05 0.06 0.04 0.02 0.03 0.03

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0140493557 NA 5.13E-06 mr1286 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
vg0140493557 4.51E-06 4.50E-06 mr1293 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
vg0140493557 3.76E-06 3.76E-06 mr1294 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
vg0140493557 1.10E-06 1.10E-06 mr1315 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
vg0140493557 NA 2.02E-06 mr1418 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
vg0140493557 NA 4.32E-06 mr1432 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
vg0140493557 4.82E-06 4.82E-06 mr1444 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
vg0140493557 NA 8.81E-07 mr1510 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
vg0140493557 NA 9.16E-09 mr1595 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
vg0140493557 NA 4.29E-06 mr1595 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
vg0140493557 NA 1.21E-06 mr1629 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
vg0140493557 NA 7.04E-10 mr1637 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
vg0140493557 NA 2.77E-06 mr1665 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
vg0140493557 9.24E-06 9.24E-06 mr1700 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
vg0140493557 NA 5.49E-06 mr1749 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
vg0140493557 NA 1.67E-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
vg0140493557 5.07E-06 5.07E-06 mr1810 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
vg0140493557 NA 8.57E-06 mr1860 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
vg0140493557 1.82E-06 1.82E-06 mr1894 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
vg0140493557 NA 1.50E-06 mr1976 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
vg0140493557 NA 6.21E-06 mr1361_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