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Detailed information for vg0104992072:

Variant ID: vg0104992072 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 4992072
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.98, G: 0.02, others allele: 0.00, population size: 250. )

Flanking Sequence (100 bp) in Reference Genome:


AGATTTTTGTCTGAAATTCTTCTAGGGTGGTTTGGTTTGACGAAGTTTGTGGAACTAGCAGCTTCAATGCATGAAGAATTGGTTTTTCAGAACTTGGACA[A/G]
GTTTGAAAAATCATGTGAGATGTTTGGAGCTTGAATACGGCCTAACATTATTTGTCCGAAATCCTTCCAAAGTGTCTGAAAATTTTTCCAAGATACAGCC

Reverse complement sequence

GGCTGTATCTTGGAAAAATTTTCAGACACTTTGGAAGGATTTCGGACAAATAATGTTAGGCCGTATTCAAGCTCCAAACATCTCACATGATTTTTCAAAC[T/C]
TGTCCAAGTTCTGAAAAACCAATTCTTCATGCATTGAAGCTGCTAGTTCCACAAACTTCGTCAAACCAAACCACCCTAGAAGAATTTCAGACAAAAATCT

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 50.50% 49.00% 0.38% 0.08% NA
All Indica  2759 79.30% 20.20% 0.47% 0.07% NA
All Japonica  1512 1.00% 98.90% 0.13% 0.00% NA
Aus  269 35.70% 63.60% 0.74% 0.00% NA
Indica I  595 43.00% 56.10% 0.67% 0.17% NA
Indica II  465 93.10% 6.50% 0.43% 0.00% NA
Indica III  913 96.40% 3.50% 0.11% 0.00% NA
Indica Intermediate  786 78.60% 20.50% 0.76% 0.13% NA
Temperate Japonica  767 1.00% 99.00% 0.00% 0.00% NA
Tropical Japonica  504 0.80% 99.00% 0.20% 0.00% NA
Japonica Intermediate  241 1.20% 98.30% 0.41% 0.00% NA
VI/Aromatic  96 45.80% 52.10% 1.04% 1.04% NA
Intermediate  90 48.90% 50.00% 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
vg0104992072 A -> G LOC_Os01g09680.1 upstream_gene_variant ; 3871.0bp to feature; MODIFIER silent_mutation Average:74.326; most accessible tissue: Zhenshan97 panicle, score: 84.374 N N N N
vg0104992072 A -> G LOC_Os01g09690.1 intron_variant ; MODIFIER silent_mutation Average:74.326; most accessible tissue: Zhenshan97 panicle, score: 84.374 N N N N
vg0104992072 A -> DEL N N silent_mutation Average:74.326; most accessible tissue: Zhenshan97 panicle, score: 84.374 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)
vg0104992072 A G 0.01 0.0 0.01 0.0 0.0 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0104992072 NA 5.15E-10 mr1663 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
vg0104992072 NA 3.43E-06 mr1295_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
vg0104992072 NA 7.08E-08 mr1527_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
vg0104992072 1.53E-07 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
vg0104992072 5.79E-07 3.03E-06 mr1587_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