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Detailed information for vg1206349677:

Variant ID: vg1206349677 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 6349677
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.93, A: 0.07, others allele: 0.00, population size: 72. )

Flanking Sequence (100 bp) in Reference Genome:


TTCCAGGATACCACAGCGGACATCATTGGTCCCTCATAGCTGGGAGGTGTGCCCGTGCAGACGCAGGACCAGTCGCCCTCCCCCCTGCTGCTAGAGCCTC[G/A]
TGCTACCCGTGCTATGCCACCGAATCGCTTCATGTACTCCTAGGATCACGTGCGAGCGCATGCCCAGAGGACCAAGCGGGGTCGTGGCATGGGGCAGAGC

Reverse complement sequence

GCTCTGCCCCATGCCACGACCCCGCTTGGTCCTCTGGGCATGCGCTCGCACGTGATCCTAGGAGTACATGAAGCGATTCGGTGGCATAGCACGGGTAGCA[C/T]
GAGGCTCTAGCAGCAGGGGGGAGGGCGACTGGTCCTGCGTCTGCACGGGCACACCTCCCAGCTATGAGGGACCAATGATGTCCGCTGTGGTATCCTGGAA

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 20.90% 18.00% 1.27% 59.88% NA
All Indica  2759 12.60% 26.10% 1.30% 59.95% NA
All Japonica  1512 38.00% 2.20% 1.32% 58.40% NA
Aus  269 17.10% 1.50% 0.74% 80.67% NA
Indica I  595 17.50% 73.60% 0.50% 8.40% NA
Indica II  465 5.20% 15.30% 0.86% 78.71% NA
Indica III  913 11.90% 1.40% 2.63% 84.01% NA
Indica Intermediate  786 14.10% 25.30% 0.64% 59.92% NA
Temperate Japonica  767 48.00% 3.70% 0.65% 47.72% NA
Tropical Japonica  504 18.10% 0.60% 2.38% 78.97% NA
Japonica Intermediate  241 48.10% 1.20% 1.24% 49.38% NA
VI/Aromatic  96 0.00% 68.80% 1.04% 30.21% NA
Intermediate  90 20.00% 26.70% 1.11% 52.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1206349677 G -> DEL N N silent_mutation Average:74.305; most accessible tissue: Minghui63 young leaf, score: 84.814 N N N N
vg1206349677 G -> A LOC_Os12g11690.1 upstream_gene_variant ; 2558.0bp to feature; MODIFIER silent_mutation Average:74.305; most accessible tissue: Minghui63 young leaf, score: 84.814 N N N N
vg1206349677 G -> A LOC_Os12g11710.1 upstream_gene_variant ; 4479.0bp to feature; MODIFIER silent_mutation Average:74.305; most accessible tissue: Minghui63 young leaf, score: 84.814 N N N N
vg1206349677 G -> A LOC_Os12g11700.1 intron_variant ; MODIFIER silent_mutation Average:74.305; most accessible tissue: Minghui63 young leaf, score: 84.814 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)
vg1206349677 G A -0.01 -0.01 -0.01 0.0 -0.01 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1206349677 NA 5.85E-06 mr1772 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
vg1206349677 NA 3.03E-11 mr1138_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
vg1206349677 3.82E-06 NA mr1950_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
vg1206349677 NA 7.31E-06 mr1950_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