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Detailed information for vg0304654587:

Variant ID: vg0304654587 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 4654587
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 268. )

Flanking Sequence (100 bp) in Reference Genome:


ATAACCGCATTGGCGCATTGCATGCTTGGATGGAGCACGTACTTTTAGTTTTTTTACTGTACTCATTTACTACCGCCTTTGGCTACCTGGCGTGCTTACT[G/A]
CTAGTACTGTAGCAAAGTAGCAAGAAGTGGAACGAGCCTAGAGGACGAAATTGATATAGGGTAATTAACGAAGGATCAAGGATGTAAATTTTAAGCCGCC

Reverse complement sequence

GGCGGCTTAAAATTTACATCCTTGATCCTTCGTTAATTACCCTATATCAATTTCGTCCTCTAGGCTCGTTCCACTTCTTGCTACTTTGCTACAGTACTAG[C/T]
AGTAAGCACGCCAGGTAGCCAAAGGCGGTAGTAAATGAGTACAGTAAAAAAACTAAAAGTACGTGCTCCATCCAAGCATGCAATGCGCCAATGCGGTTAT

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 50.90% 48.90% 0.00% 0.19% NA
All Indica  2759 22.80% 77.10% 0.00% 0.11% NA
All Japonica  1512 97.30% 2.40% 0.00% 0.26% NA
Aus  269 58.00% 42.00% 0.00% 0.00% NA
Indica I  595 11.60% 88.40% 0.00% 0.00% NA
Indica II  465 25.20% 74.60% 0.00% 0.22% NA
Indica III  913 26.50% 73.50% 0.00% 0.00% NA
Indica Intermediate  786 25.70% 74.00% 0.00% 0.25% NA
Temperate Japonica  767 99.70% 0.30% 0.00% 0.00% NA
Tropical Japonica  504 92.70% 6.90% 0.00% 0.40% NA
Japonica Intermediate  241 99.20% 0.00% 0.00% 0.83% NA
VI/Aromatic  96 94.80% 4.20% 0.00% 1.04% NA
Intermediate  90 63.30% 35.60% 0.00% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0304654587 G -> A LOC_Os03g08960.1 3_prime_UTR_variant ; 154.0bp to feature; MODIFIER silent_mutation Average:94.837; most accessible tissue: Minghui63 young leaf, score: 98.795 N N N N
vg0304654587 G -> DEL N N silent_mutation Average:94.837; most accessible tissue: Minghui63 young leaf, score: 98.795 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)
vg0304654587 G A 0.02 -0.01 0.0 -0.05 -0.01 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0304654587 6.36E-06 NA mr1739 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
vg0304654587 3.51E-06 NA mr1739 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
vg0304654587 NA 2.12E-07 mr1053_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
vg0304654587 NA 1.42E-06 mr1144_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
vg0304654587 NA 6.36E-09 mr1299_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
vg0304654587 NA 6.11E-06 mr1381_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
vg0304654587 NA 4.32E-06 mr1541_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
vg0304654587 NA 5.83E-09 mr1624_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
vg0304654587 NA 1.06E-08 mr1700_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
vg0304654587 NA 8.88E-13 mr1713_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
vg0304654587 NA 2.11E-07 mr1727_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
vg0304654587 NA 7.44E-10 mr1756_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
vg0304654587 NA 1.39E-06 mr1785_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
vg0304654587 NA 1.36E-07 mr1804_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
vg0304654587 NA 3.48E-07 mr1837_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
vg0304654587 NA 2.88E-07 mr1842_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
vg0304654587 NA 1.63E-06 mr1915_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