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Detailed information for vg1222451825:

Variant ID: vg1222451825 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 22451825
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.72, A: 0.28, others allele: 0.00, population size: 61. )

Flanking Sequence (100 bp) in Reference Genome:


ATGGCAGGAAGCGTTGTGCAACCTCTGAATTTTAATTGGTACTAGTAGTTTGGTACTACGAAGTATTACTACGCAAGTGCTTTTATCTGACGGTTGATCG[G/A]
CCATCAAGAAAGATCTCCATCCTGACAGTGACTTGTTCCGTAAGTGTCAGTCATTCAGGCGATTGATGTATTGTGTTTGGCTCCAGTCTTTGCTCTGATC

Reverse complement sequence

GATCAGAGCAAAGACTGGAGCCAAACACAATACATCAATCGCCTGAATGACTGACACTTACGGAACAAGTCACTGTCAGGATGGAGATCTTTCTTGATGG[C/T]
CGATCAACCGTCAGATAAAAGCACTTGCGTAGTAATACTTCGTAGTACCAAACTACTAGTACCAATTAAAATTCAGAGGTTGCACAACGCTTCCTGCCAT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 53.20% 36.70% 9.44% 0.70% NA
All Indica  2759 35.50% 51.80% 11.53% 1.20% NA
All Japonica  1512 83.70% 8.10% 8.27% 0.00% NA
Aus  269 37.20% 62.50% 0.37% 0.00% NA
Indica I  595 58.30% 38.30% 3.19% 0.17% NA
Indica II  465 23.20% 74.60% 1.94% 0.22% NA
Indica III  913 30.00% 44.60% 23.66% 1.75% NA
Indica Intermediate  786 31.90% 56.70% 9.41% 1.91% NA
Temperate Japonica  767 85.80% 11.30% 2.87% 0.00% NA
Tropical Japonica  504 77.80% 3.80% 18.45% 0.00% NA
Japonica Intermediate  241 89.20% 6.60% 4.15% 0.00% NA
VI/Aromatic  96 96.90% 3.10% 0.00% 0.00% NA
Intermediate  90 83.30% 14.40% 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
vg1222451825 G -> DEL N N silent_mutation Average:86.087; most accessible tissue: Minghui63 young leaf, score: 93.26 N N N N
vg1222451825 G -> A LOC_Os12g36660.1 downstream_gene_variant ; 2551.0bp to feature; MODIFIER silent_mutation Average:86.087; most accessible tissue: Minghui63 young leaf, score: 93.26 N N N N
vg1222451825 G -> A LOC_Os12g36660-LOC_Os12g36670 intergenic_region ; MODIFIER silent_mutation Average:86.087; most accessible tissue: Minghui63 young leaf, score: 93.26 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)
vg1222451825 G A -0.05 -0.08 -0.16 -0.06 -0.12 -0.19

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1222451825 NA 8.00E-06 mr1074_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
vg1222451825 3.49E-06 3.49E-06 mr1821_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
vg1222451825 NA 7.38E-06 mr1882_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
vg1222451825 NA 5.40E-06 mr1882_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