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Detailed information for vg0229433488:

Variant ID: vg0229433488 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 29433488
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AGGCTGTTTCTTTTTTTTTTCCCTCCGTTCTCACGTACTCTCTCCGTCCACAAGCTATGGGTTTTCGTATGGGTTTTCGTATCCAACTTTGACTGTTCGT[C/T]
TTATATGAAATTTTTTTTAATTCGTACTTGCGTTGTTGTTAGATGATAAAACATGATTAATATTTTATGCGTGACTTATCTTTTTAATTTTTTTCATAAT

Reverse complement sequence

ATTATGAAAAAAATTAAAAAGATAAGTCACGCATAAAATATTAATCATGTTTTATCATCTAACAACAACGCAAGTACGAATTAAAAAAAATTTCATATAA[G/A]
ACGAACAGTCAAAGTTGGATACGAAAACCCATACGAAAACCCATAGCTTGTGGACGGAGAGAGTACGTGAGAACGGAGGGAAAAAAAAAAGAAACAGCCT

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 78.30% 21.50% 0.15% 0.00% NA
All Indica  2759 97.00% 3.00% 0.00% 0.00% NA
All Japonica  1512 62.10% 37.60% 0.26% 0.00% NA
Aus  269 8.90% 90.70% 0.37% 0.00% NA
Indica I  595 99.70% 0.30% 0.00% 0.00% NA
Indica II  465 99.60% 0.40% 0.00% 0.00% NA
Indica III  913 97.70% 2.30% 0.00% 0.00% NA
Indica Intermediate  786 92.70% 7.30% 0.00% 0.00% NA
Temperate Japonica  767 82.50% 16.90% 0.52% 0.00% NA
Tropical Japonica  504 25.80% 74.20% 0.00% 0.00% NA
Japonica Intermediate  241 73.00% 27.00% 0.00% 0.00% NA
VI/Aromatic  96 4.20% 94.80% 1.04% 0.00% NA
Intermediate  90 63.30% 35.60% 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
vg0229433488 C -> T LOC_Os02g48094.1 upstream_gene_variant ; 4844.0bp to feature; MODIFIER silent_mutation Average:83.378; most accessible tissue: Minghui63 root, score: 95.002 N N N N
vg0229433488 C -> T LOC_Os02g48080.1 downstream_gene_variant ; 1028.0bp to feature; MODIFIER silent_mutation Average:83.378; most accessible tissue: Minghui63 root, score: 95.002 N N N N
vg0229433488 C -> T LOC_Os02g48090.1 downstream_gene_variant ; 539.0bp to feature; MODIFIER silent_mutation Average:83.378; most accessible tissue: Minghui63 root, score: 95.002 N N N N
vg0229433488 C -> T LOC_Os02g48080-LOC_Os02g48090 intergenic_region ; MODIFIER silent_mutation Average:83.378; most accessible tissue: Minghui63 root, score: 95.002 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)
vg0229433488 C T 0.0 0.02 0.01 0.01 0.01 0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0229433488 NA 6.37E-10 mr1029 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
vg0229433488 NA 3.51E-13 mr1047 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
vg0229433488 NA 3.53E-06 mr1057 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
vg0229433488 NA 1.03E-10 mr1189 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
vg0229433488 NA 3.61E-10 mr1625 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
vg0229433488 NA 1.10E-07 mr1642 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
vg0229433488 NA 3.51E-06 mr1684 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
vg0229433488 NA 1.33E-07 mr1725 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
vg0229433488 NA 1.85E-07 mr1734 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
vg0229433488 NA 1.99E-08 mr1796 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
vg0229433488 NA 2.51E-07 mr1990 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
vg0229433488 NA 1.91E-16 mr1047_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
vg0229433488 NA 6.71E-21 mr1189_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
vg0229433488 NA 6.74E-12 mr1642_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
vg0229433488 NA 2.65E-09 mr1649_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
vg0229433488 NA 3.51E-16 mr1734_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
vg0229433488 NA 2.31E-14 mr1782_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
vg0229433488 NA 1.14E-06 mr1815_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