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Detailed information for vg0201029471:

Variant ID: vg0201029471 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 1029471
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 117. )

Flanking Sequence (100 bp) in Reference Genome:


TATAGCTAATCCAATAGCTTATTCATACAATAGTTAACCATAGAAATATTCTACACCATTAATATCACCTCTCATACACACATAACATTTTAGAGTCTGT[G/A]
TTCCAGCTGGCTATAAATCTGTAGCCGCTTTCTTTTCTCTCTTCTCTTTTCTTCTCGATATGTTGTGATTATAGCTGGCTTATAGCTTTTCCTGCTCTAA

Reverse complement sequence

TTAGAGCAGGAAAAGCTATAAGCCAGCTATAATCACAACATATCGAGAAGAAAAGAGAAGAGAGAAAAGAAAGCGGCTACAGATTTATAGCCAGCTGGAA[C/T]
ACAGACTCTAAAATGTTATGTGTGTATGAGAGGTGATATTAATGGTGTAGAATATTTCTATGGTTAACTATTGTATGAATAAGCTATTGGATTAGCTATA

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 75.80% 24.10% 0.08% 0.02% NA
All Indica  2759 59.10% 40.70% 0.14% 0.04% NA
All Japonica  1512 99.70% 0.30% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 10.40% 89.40% 0.17% 0.00% NA
Indica II  465 61.50% 38.10% 0.43% 0.00% NA
Indica III  913 89.60% 10.40% 0.00% 0.00% NA
Indica Intermediate  786 59.20% 40.60% 0.13% 0.13% NA
Temperate Japonica  767 99.70% 0.30% 0.00% 0.00% NA
Tropical Japonica  504 99.60% 0.40% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 87.80% 12.20% 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
vg0201029471 G -> A LOC_Os02g02720.3 upstream_gene_variant ; 4720.0bp to feature; MODIFIER silent_mutation Average:72.441; most accessible tissue: Zhenshan97 panicle, score: 93.02 N N N N
vg0201029471 G -> A LOC_Os02g02730.1 upstream_gene_variant ; 454.0bp to feature; MODIFIER silent_mutation Average:72.441; most accessible tissue: Zhenshan97 panicle, score: 93.02 N N N N
vg0201029471 G -> A LOC_Os02g02720.4 upstream_gene_variant ; 4720.0bp to feature; MODIFIER silent_mutation Average:72.441; most accessible tissue: Zhenshan97 panicle, score: 93.02 N N N N
vg0201029471 G -> A LOC_Os02g02720.5 upstream_gene_variant ; 4720.0bp to feature; MODIFIER silent_mutation Average:72.441; most accessible tissue: Zhenshan97 panicle, score: 93.02 N N N N
vg0201029471 G -> A LOC_Os02g02720.1 upstream_gene_variant ; 4720.0bp to feature; MODIFIER silent_mutation Average:72.441; most accessible tissue: Zhenshan97 panicle, score: 93.02 N N N N
vg0201029471 G -> A LOC_Os02g02720.2 upstream_gene_variant ; 4758.0bp to feature; MODIFIER silent_mutation Average:72.441; most accessible tissue: Zhenshan97 panicle, score: 93.02 N N N N
vg0201029471 G -> A LOC_Os02g02720-LOC_Os02g02730 intergenic_region ; MODIFIER silent_mutation Average:72.441; most accessible tissue: Zhenshan97 panicle, score: 93.02 N N N N
vg0201029471 G -> DEL N N silent_mutation Average:72.441; most accessible tissue: Zhenshan97 panicle, score: 93.02 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)
vg0201029471 G A -0.02 -0.01 -0.01 -0.02 -0.01 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0201029471 NA 1.20E-07 mr1072 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
vg0201029471 NA 2.00E-06 mr1075 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
vg0201029471 NA 2.71E-19 mr1077 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
vg0201029471 NA 2.81E-06 mr1080 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
vg0201029471 NA 2.11E-08 mr1100 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
vg0201029471 NA 2.88E-07 mr1124 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
vg0201029471 NA 4.92E-06 mr1202 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
vg0201029471 NA 1.37E-08 mr1342 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
vg0201029471 NA 1.19E-08 mr1457 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
vg0201029471 NA 3.51E-07 mr1613 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
vg0201029471 NA 8.19E-07 mr1619 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
vg0201029471 NA 4.55E-10 mr1717 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
vg0201029471 NA 2.87E-10 mr1770 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
vg0201029471 NA 2.27E-07 mr1842 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
vg0201029471 NA 3.83E-07 mr1861 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
vg0201029471 NA 3.46E-07 mr1962 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
vg0201029471 NA 6.30E-06 mr1123_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
vg0201029471 NA 1.88E-07 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
vg0201029471 NA 1.92E-06 mr1242_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
vg0201029471 NA 2.08E-07 mr1272_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
vg0201029471 NA 8.96E-20 mr1531_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
vg0201029471 NA 1.98E-07 mr1936_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