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Detailed information for vg0132071481:

Variant ID: vg0132071481 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 32071481
Reference Allele: TAlternative Allele: C,A
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.77, T: 0.23, others allele: 0.00, population size: 92. )

Flanking Sequence (100 bp) in Reference Genome:


TTCATGATAAGTACTCCCTCCGTCCCAAAATATAGCAACTTTTGGTTGGATGGGATAAATCTTAGTACTAACGAATCTGGACATGCCTCTATGTCCCATC[T/C,A]
AACTAAAAGTTGCTATATTTTGGAACGGAGGGAGTAGTATTTTTGCGTTCAGTTTAGAGGGGCAGCAAAGAGGACTGGAGTCTGGAGGGTGCAATTCTAC

Reverse complement sequence

GTAGAATTGCACCCTCCAGACTCCAGTCCTCTTTGCTGCCCCTCTAAACTGAACGCAAAAATACTACTCCCTCCGTTCCAAAATATAGCAACTTTTAGTT[A/G,T]
GATGGGACATAGAGGCATGTCCAGATTCGTTAGTACTAAGATTTATCCCATCCAACCAAAAGTTGCTATATTTTGGGACGGAGGGAGTACTTATCATGAA

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 79.10% 20.80% 0.02% 0.00% A: 0.02%
All Indica  2759 98.10% 1.90% 0.00% 0.00% A: 0.04%
All Japonica  1512 40.50% 59.50% 0.00% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 97.00% 3.00% 0.00% 0.00% NA
Indica II  465 98.70% 1.10% 0.00% 0.00% A: 0.22%
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 96.30% 3.70% 0.00% 0.00% NA
Temperate Japonica  767 4.30% 95.70% 0.00% 0.00% NA
Tropical Japonica  504 89.70% 10.30% 0.00% 0.00% NA
Japonica Intermediate  241 52.70% 47.30% 0.00% 0.00% NA
VI/Aromatic  96 89.60% 10.40% 0.00% 0.00% NA
Intermediate  90 74.40% 24.40% 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
vg0132071481 T -> A LOC_Os01g55660.1 upstream_gene_variant ; 1635.0bp to feature; MODIFIER silent_mutation Average:85.156; most accessible tissue: Callus, score: 93.166 N N N N
vg0132071481 T -> A LOC_Os01g55700.1 downstream_gene_variant ; 968.0bp to feature; MODIFIER silent_mutation Average:85.156; most accessible tissue: Callus, score: 93.166 N N N N
vg0132071481 T -> A LOC_Os01g55670.1 intron_variant ; MODIFIER silent_mutation Average:85.156; most accessible tissue: Callus, score: 93.166 N N N N
vg0132071481 T -> C LOC_Os01g55660.1 upstream_gene_variant ; 1635.0bp to feature; MODIFIER silent_mutation Average:85.156; most accessible tissue: Callus, score: 93.166 N N N N
vg0132071481 T -> C LOC_Os01g55700.1 downstream_gene_variant ; 968.0bp to feature; MODIFIER silent_mutation Average:85.156; most accessible tissue: Callus, score: 93.166 N N N N
vg0132071481 T -> C LOC_Os01g55670.1 intron_variant ; MODIFIER silent_mutation Average:85.156; most accessible tissue: Callus, score: 93.166 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)
vg0132071481 T A -0.01 -0.02 -0.01 -0.02 -0.02 -0.01
vg0132071481 T C 0.0 -0.01 -0.01 -0.01 -0.01 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0132071481 NA 2.27E-13 mr1010 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
vg0132071481 NA 1.09E-12 mr1056 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
vg0132071481 NA 8.34E-22 mr1115 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
vg0132071481 NA 2.31E-23 mr1163 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
vg0132071481 NA 3.81E-10 mr1277 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
vg0132071481 NA 3.94E-10 mr1449 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
vg0132071481 NA 4.66E-07 mr1543 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
vg0132071481 NA 5.86E-13 mr1740 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
vg0132071481 NA 4.26E-15 mr1844 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
vg0132071481 NA 2.55E-07 mr1871 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
vg0132071481 NA 6.04E-23 mr1920 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
vg0132071481 NA 4.55E-11 mr1042_2 Jap_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
vg0132071481 NA 8.90E-18 mr1156_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
vg0132071481 NA 8.30E-07 mr1229_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
vg0132071481 NA 1.81E-06 mr1359_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
vg0132071481 NA 1.58E-06 mr1363_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
vg0132071481 NA 1.14E-09 mr1502_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
vg0132071481 NA 6.10E-08 mr1526_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
vg0132071481 NA 8.18E-13 mr1543_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
vg0132071481 NA 4.52E-06 mr1582_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
vg0132071481 NA 8.19E-09 mr1680_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
vg0132071481 NA 1.00E-14 mr1742_2 Jap_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
vg0132071481 NA 1.39E-08 mr1808_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
vg0132071481 NA 2.98E-12 mr1844_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
vg0132071481 9.49E-08 NA mr1871_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
vg0132071481 NA 6.16E-14 mr1871_2 Jap_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
vg0132071481 NA 7.42E-09 mr1952_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