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Detailed information for vg0314573659:

Variant ID: vg0314573659 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 14573659
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 122. )

Flanking Sequence (100 bp) in Reference Genome:


CTGGTGGTGACGGCGAAGGCGGCGGCGGCGGCTTCGGCATCGGCCGTGGCTGGTTGCGGCGGCGGCGGCGGGTGACCGGTTGCTTTGATGGTGGCAGCAA[C/T]
TGGCGACCGGCTTCTTTTTTAACGACAGCTGGTGACGGTGGCGGGCAAGCAGCTTCTGCTTTGACGGTGGTGGGTGACGGTGGCGGTGGCTGTCACACCC

Reverse complement sequence

GGGTGTGACAGCCACCGCCACCGTCACCCACCACCGTCAAAGCAGAAGCTGCTTGCCCGCCACCGTCACCAGCTGTCGTTAAAAAAGAAGCCGGTCGCCA[G/A]
TTGCTGCCACCATCAAAGCAACCGGTCACCCGCCGCCGCCGCCGCAACCAGCCACGGCCGATGCCGAAGCCGCCGCCGCCGCCTTCGCCGTCACCACCAG

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 73.70% 24.00% 2.09% 0.23% NA
All Indica  2759 57.00% 40.40% 2.61% 0.00% NA
All Japonica  1512 97.60% 0.20% 1.52% 0.73% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 52.60% 41.80% 5.55% 0.00% NA
Indica II  465 80.90% 18.50% 0.65% 0.00% NA
Indica III  913 44.50% 54.70% 0.88% 0.00% NA
Indica Intermediate  786 60.80% 35.60% 3.56% 0.00% NA
Temperate Japonica  767 95.80% 0.00% 2.87% 1.30% NA
Tropical Japonica  504 99.40% 0.40% 0.20% 0.00% NA
Japonica Intermediate  241 99.20% 0.40% 0.00% 0.41% NA
VI/Aromatic  96 95.80% 4.20% 0.00% 0.00% NA
Intermediate  90 80.00% 15.60% 4.44% 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
vg0314573659 C -> T LOC_Os03g25530.1 upstream_gene_variant ; 4880.0bp to feature; MODIFIER silent_mutation Average:65.272; most accessible tissue: Zhenshan97 flag leaf, score: 90.181 N N N N
vg0314573659 C -> T LOC_Os03g25500.1 downstream_gene_variant ; 1896.0bp to feature; MODIFIER silent_mutation Average:65.272; most accessible tissue: Zhenshan97 flag leaf, score: 90.181 N N N N
vg0314573659 C -> T LOC_Os03g25510.1 downstream_gene_variant ; 871.0bp to feature; MODIFIER silent_mutation Average:65.272; most accessible tissue: Zhenshan97 flag leaf, score: 90.181 N N N N
vg0314573659 C -> T LOC_Os03g25500-LOC_Os03g25510 intergenic_region ; MODIFIER silent_mutation Average:65.272; most accessible tissue: Zhenshan97 flag leaf, score: 90.181 N N N N
vg0314573659 C -> DEL N N silent_mutation Average:65.272; most accessible tissue: Zhenshan97 flag leaf, score: 90.181 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)
vg0314573659 C T -0.02 0.0 0.01 -0.01 -0.01 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0314573659 NA 3.92E-06 mr1130 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
vg0314573659 3.67E-46 NA mr1542 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
vg0314573659 5.29E-41 1.12E-62 mr1542 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
vg0314573659 NA 2.46E-07 mr1902 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
vg0314573659 2.17E-44 NA mr1542_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
vg0314573659 6.38E-44 9.84E-69 mr1542_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
vg0314573659 2.58E-08 NA mr1587_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
vg0314573659 3.42E-09 8.48E-12 mr1587_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