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Detailed information for vg0921003290:

Variant ID: vg0921003290 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 21003290
Reference Allele: AAlternative Allele: C
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, A: 0.02, others allele: 0.00, population size: 115. )

Flanking Sequence (100 bp) in Reference Genome:


GGGCCAACCAAGCGGGTTAGCGGCACAACCCGCCCCACCTTGAACCCGAGGAACCAATGCAAGGCGACCAGAAGAAGGTGGGGACCCACGTCAGCGCAAG[A/C]
AAGCCCGTCCCCGATGATGTTGGTCGCGATCGCCGTGGAGACGTACGGCGACCGAGCCGGCCGATATCCGTGGCCCGCAACGAGATCAAGGCAGGTGGCG

Reverse complement sequence

CGCCACCTGCCTTGATCTCGTTGCGGGCCACGGATATCGGCCGGCTCGGTCGCCGTACGTCTCCACGGCGATCGCGACCAACATCATCGGGGACGGGCTT[T/G]
CTTGCGCTGACGTGGGTCCCCACCTTCTTCTGGTCGCCTTGCATTGGTTCCTCGGGTTCAAGGTGGGGCGGGTTGTGCCGCTAACCCGCTTGGTTGGCCC

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 51.30% 48.40% 0.25% 0.08% NA
All Indica  2759 80.00% 19.60% 0.29% 0.14% NA
All Japonica  1512 0.20% 99.70% 0.13% 0.00% NA
Aus  269 68.40% 31.60% 0.00% 0.00% NA
Indica I  595 86.20% 12.80% 0.67% 0.34% NA
Indica II  465 93.80% 6.00% 0.22% 0.00% NA
Indica III  913 73.50% 26.50% 0.00% 0.00% NA
Indica Intermediate  786 74.60% 24.80% 0.38% 0.25% NA
Temperate Japonica  767 0.10% 99.70% 0.13% 0.00% NA
Tropical Japonica  504 0.00% 99.80% 0.20% 0.00% NA
Japonica Intermediate  241 0.80% 99.20% 0.00% 0.00% NA
VI/Aromatic  96 7.30% 92.70% 0.00% 0.00% NA
Intermediate  90 26.70% 71.10% 2.22% 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
vg0921003290 A -> DEL N N silent_mutation Average:79.048; most accessible tissue: Callus, score: 97.599 N N N N
vg0921003290 A -> C LOC_Os09g36410.1 upstream_gene_variant ; 4723.0bp to feature; MODIFIER silent_mutation Average:79.048; most accessible tissue: Callus, score: 97.599 N N N N
vg0921003290 A -> C LOC_Os09g36400.1 intron_variant ; MODIFIER silent_mutation Average:79.048; most accessible tissue: Callus, score: 97.599 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)
vg0921003290 A C 0.0 -0.06 -0.08 -0.1 -0.12 -0.12

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0921003290 NA 2.49E-06 mr1011 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
vg0921003290 NA 2.18E-07 mr1627 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
vg0921003290 NA 7.43E-08 mr1084_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
vg0921003290 NA 6.94E-06 mr1105_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
vg0921003290 NA 3.03E-07 mr1180_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
vg0921003290 NA 4.38E-06 mr1296_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
vg0921003290 NA 8.90E-06 mr1331_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
vg0921003290 NA 4.82E-08 mr1378_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
vg0921003290 NA 4.74E-14 mr1454_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
vg0921003290 NA 6.83E-06 mr1454_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
vg0921003290 NA 8.29E-14 mr1521_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
vg0921003290 NA 7.06E-23 mr1627_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
vg0921003290 NA 1.57E-09 mr1627_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
vg0921003290 NA 2.13E-12 mr1739_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
vg0921003290 NA 5.33E-06 mr1793_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
vg0921003290 NA 4.53E-06 mr1944_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