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Detailed information for vg0308219850:

Variant ID: vg0308219850 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 8219850
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 331. )

Flanking Sequence (100 bp) in Reference Genome:


CGAGCATGGCGGCGTACTTGGTCGGGTGGAGCATGATGAACGCTGCACCGAAGCAAGCAGAGAACGTAGCCTGCGGCTCCTTGATGCCATCCTCCGTGCC[G/A]
GCAACCTGTTGAAATGGCAATGCAATAACGAAGATTCAGGCTAAATTCCTTTGTTGATCATCAAGGTGATAGGAAGGTAAGGCAGGTGACTCTGCTTCTG

Reverse complement sequence

CAGAAGCAGAGTCACCTGCCTTACCTTCCTATCACCTTGATGATCAACAAAGGAATTTAGCCTGAATCTTCGTTATTGCATTGCCATTTCAACAGGTTGC[C/T]
GGCACGGAGGATGGCATCAAGGAGCCGCAGGCTACGTTCTCTGCTTGCTTCGGTGCAGCGTTCATCATGCTCCACCCGACCAAGTACGCCGCCATGCTCG

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 85.00% 14.90% 0.06% 0.00% NA
All Indica  2759 99.60% 0.40% 0.00% 0.00% NA
All Japonica  1512 55.30% 44.50% 0.20% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 99.50% 0.50% 0.00% 0.00% NA
Indica Intermediate  786 99.50% 0.50% 0.00% 0.00% NA
Temperate Japonica  767 54.40% 45.20% 0.39% 0.00% NA
Tropical Japonica  504 42.50% 57.50% 0.00% 0.00% NA
Japonica Intermediate  241 85.10% 14.90% 0.00% 0.00% NA
VI/Aromatic  96 91.70% 8.30% 0.00% 0.00% NA
Intermediate  90 84.40% 15.60% 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
vg0308219850 G -> A LOC_Os03g15050.1 synonymous_variant ; p.Ala505Ala; LOW synonymous_codon Average:91.168; most accessible tissue: Zhenshan97 young leaf, score: 96.823 N N N N
vg0308219850 G -> A LOC_Os03g15050.4 synonymous_variant ; p.Ala297Ala; LOW synonymous_codon Average:91.168; most accessible tissue: Zhenshan97 young leaf, score: 96.823 N N N N
vg0308219850 G -> A LOC_Os03g15050.2 synonymous_variant ; p.Ala505Ala; LOW synonymous_codon Average:91.168; most accessible tissue: Zhenshan97 young leaf, score: 96.823 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)
vg0308219850 G A -0.01 0.0 -0.03 0.0 0.0 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0308219850 NA 4.06E-07 mr1779 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
vg0308219850 1.52E-06 4.32E-10 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
vg0308219850 9.16E-06 9.19E-09 mr1355_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
vg0308219850 NA 2.17E-06 mr1470_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
vg0308219850 NA 1.30E-08 mr1749_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
vg0308219850 NA 1.79E-09 mr1821_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
vg0308219850 NA 2.47E-06 mr1899_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