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Detailed information for vg0524346743:

Variant ID: vg0524346743 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 24346743
Reference Allele: CAlternative Allele: A,T
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AAATTGGTATGTCTGATACTAGTCGTTCGAAAAATAGGGCCTTTTGTGCAAATTCAAACTTAGGACCTGTTTAGTTCGCGAAATAAAAATTTTTAGGTGT[C/A,T]
ACATCGAACGTTTGATTAGATTTCGGAAAAGGTTTTTGGACACGAATGAAAAAACTAATTTCATAAATCGCCTGGAAACCGCGAGACGAATCTTTTGAGT

Reverse complement sequence

ACTCAAAAGATTCGTCTCGCGGTTTCCAGGCGATTTATGAAATTAGTTTTTTCATTCGTGTCCAAAAACCTTTTCCGAAATCTAATCAAACGTTCGATGT[G/T,A]
ACACCTAAAAATTTTTATTTCGCGAACTAAACAGGTCCTAAGTTTGAATTTGCACAAAAGGCCCTATTTTTCGAACGACTAGTATCAGACATACCAATTT

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 94.70% 5.30% 0.00% 0.00% T: 0.06%
All Indica  2759 99.10% 0.90% 0.00% 0.00% NA
All Japonica  1512 99.80% 0.00% 0.00% 0.00% T: 0.20%
Aus  269 26.00% 74.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.40% 0.60% 0.00% 0.00% NA
Indica III  913 99.30% 0.70% 0.00% 0.00% NA
Indica Intermediate  786 97.80% 2.20% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 98.80% 0.00% 0.00% 0.00% T: 1.24%
VI/Aromatic  96 80.20% 19.80% 0.00% 0.00% NA
Intermediate  90 94.40% 5.60% 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
vg0524346743 C -> T LOC_Os05g41570.1 upstream_gene_variant ; 3816.0bp to feature; MODIFIER silent_mutation Average:78.975; most accessible tissue: Minghui63 flag leaf, score: 92.129 N N N N
vg0524346743 C -> T LOC_Os05g41580.1 upstream_gene_variant ; 462.0bp to feature; MODIFIER silent_mutation Average:78.975; most accessible tissue: Minghui63 flag leaf, score: 92.129 N N N N
vg0524346743 C -> T LOC_Os05g41570-LOC_Os05g41580 intergenic_region ; MODIFIER silent_mutation Average:78.975; most accessible tissue: Minghui63 flag leaf, score: 92.129 N N N N
vg0524346743 C -> A LOC_Os05g41570.1 upstream_gene_variant ; 3816.0bp to feature; MODIFIER silent_mutation Average:78.975; most accessible tissue: Minghui63 flag leaf, score: 92.129 N N N N
vg0524346743 C -> A LOC_Os05g41580.1 upstream_gene_variant ; 462.0bp to feature; MODIFIER silent_mutation Average:78.975; most accessible tissue: Minghui63 flag leaf, score: 92.129 N N N N
vg0524346743 C -> A LOC_Os05g41570-LOC_Os05g41580 intergenic_region ; MODIFIER silent_mutation Average:78.975; most accessible tissue: Minghui63 flag leaf, score: 92.129 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)
vg0524346743 C A -0.02 -0.01 -0.02 0.0 -0.02 -0.02
vg0524346743 C T -0.02 -0.01 -0.01 0.0 -0.02 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0524346743 NA 1.52E-10 mr1499 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
vg0524346743 2.55E-11 1.58E-21 mr1612 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
vg0524346743 NA 3.93E-07 mr1706 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
vg0524346743 NA 7.08E-09 mr1989 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
vg0524346743 5.58E-09 NA mr1109_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
vg0524346743 NA 2.15E-17 mr1119_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
vg0524346743 NA 5.85E-09 mr1126_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
vg0524346743 NA 9.05E-11 mr1166_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
vg0524346743 1.82E-13 9.17E-20 mr1612_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
vg0524346743 NA 4.69E-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