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Detailed information for vg0234351254:

Variant ID: vg0234351254 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 34351254
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.55, C: 0.45, others allele: 0.00, population size: 107. )

Flanking Sequence (100 bp) in Reference Genome:


GCCCAGCTCCCAGAACACCCGCCCTTTTCCAAATCACCAAGACCAAGCACCCGTCATCCACTTCTCCCCCACTGCCAGGTGGGCCCGTACTCCACCATGG[T/C]
CCCACATGTCAGCTGAATCTTCCACTGCAAGAAGCGGGAAACATTTCGGGTGGAGGCGGGTTTCCCCCCAATTTCTCCCTCCATTTTTTTTTTCGCTTCG

Reverse complement sequence

CGAAGCGAAAAAAAAAATGGAGGGAGAAATTGGGGGGAAACCCGCCTCCACCCGAAATGTTTCCCGCTTCTTGCAGTGGAAGATTCAGCTGACATGTGGG[A/G]
CCATGGTGGAGTACGGGCCCACCTGGCAGTGGGGGAGAAGTGGATGACGGGTGCTTGGTCTTGGTGATTTGGAAAAGGGCGGGTGTTCTGGGAGCTGGGC

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 66.50% 33.30% 0.15% 0.00% NA
All Indica  2759 98.50% 1.30% 0.18% 0.00% NA
All Japonica  1512 9.70% 90.30% 0.00% 0.00% NA
Aus  269 57.60% 42.40% 0.00% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 98.10% 1.50% 0.43% 0.00% NA
Indica III  913 98.50% 1.50% 0.00% 0.00% NA
Indica Intermediate  786 97.70% 1.90% 0.38% 0.00% NA
Temperate Japonica  767 3.40% 96.60% 0.00% 0.00% NA
Tropical Japonica  504 20.60% 79.40% 0.00% 0.00% NA
Japonica Intermediate  241 7.10% 92.90% 0.00% 0.00% NA
VI/Aromatic  96 72.90% 27.10% 0.00% 0.00% NA
Intermediate  90 60.00% 37.80% 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
vg0234351254 T -> C LOC_Os02g56130.1 upstream_gene_variant ; 153.0bp to feature; MODIFIER silent_mutation Average:99.148; most accessible tissue: Callus, score: 99.892 N N N N
vg0234351254 T -> C LOC_Os02g56120.1 downstream_gene_variant ; 1398.0bp to feature; MODIFIER silent_mutation Average:99.148; most accessible tissue: Callus, score: 99.892 N N N N
vg0234351254 T -> C LOC_Os02g56140.1 downstream_gene_variant ; 2476.0bp to feature; MODIFIER silent_mutation Average:99.148; most accessible tissue: Callus, score: 99.892 N N N N
vg0234351254 T -> C LOC_Os02g56120.2 downstream_gene_variant ; 1398.0bp to feature; MODIFIER silent_mutation Average:99.148; most accessible tissue: Callus, score: 99.892 N N N N
vg0234351254 T -> C LOC_Os02g56120.3 downstream_gene_variant ; 1398.0bp to feature; MODIFIER silent_mutation Average:99.148; most accessible tissue: Callus, score: 99.892 N N N N
vg0234351254 T -> C LOC_Os02g56120-LOC_Os02g56130 intergenic_region ; MODIFIER silent_mutation Average:99.148; most accessible tissue: Callus, score: 99.892 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)
vg0234351254 T C 0.0 -0.02 0.01 0.0 0.01 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0234351254 NA 4.24E-26 mr1238 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
vg0234351254 NA 1.56E-16 mr1484 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
vg0234351254 NA 7.65E-23 mr1698 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
vg0234351254 NA 3.05E-24 mr1841 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
vg0234351254 NA 2.59E-07 mr1915 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
vg0234351254 NA 1.49E-06 mr1020_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
vg0234351254 2.39E-07 8.95E-21 mr1042_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
vg0234351254 8.63E-06 NA mr1042_2 Jap_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
vg0234351254 NA 2.03E-19 mr1167_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
vg0234351254 NA 2.58E-06 mr1227_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
vg0234351254 NA 1.20E-06 mr1275_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
vg0234351254 NA 3.87E-08 mr1335_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
vg0234351254 NA 3.68E-24 mr1386_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
vg0234351254 NA 2.20E-09 mr1478_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
vg0234351254 NA 2.01E-06 mr1479_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
vg0234351254 NA 6.62E-10 mr1506_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
vg0234351254 3.38E-07 NA mr1543_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
vg0234351254 NA 3.87E-10 mr1680_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
vg0234351254 1.17E-06 1.77E-28 mr1698_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
vg0234351254 NA 9.58E-07 mr1698_2 Jap_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
vg0234351254 NA 1.57E-11 mr1714_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
vg0234351254 NA 3.03E-16 mr1726_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
vg0234351254 4.61E-07 NA mr1742_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
vg0234351254 7.52E-06 NA mr1742_2 Jap_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
vg0234351254 2.45E-06 NA mr1871_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
vg0234351254 NA 6.05E-15 mr1950_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