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Detailed information for vg1200208711:

Variant ID: vg1200208711 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 208711
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: 313. )

Flanking Sequence (100 bp) in Reference Genome:


GTTATGATATTCTATGGGTCTCCCCATAGTCGAGTCCTCTCGTAGGTTGGCCTTTTTGCTTTCTTAGTTGGTCGGTGTCTTGGTCATGGAGGCTAGGCAT[G/A]
CAGGCGGTGAATTTAGTGGCGGTGGTTGTCAGAGGTGGTCGGGAGCCAGTGCCCTGAATCGACGGTCTTGGAGACAGCGGTCAGGAGCTGGCACCCCGAA

Reverse complement sequence

TTCGGGGTGCCAGCTCCTGACCGCTGTCTCCAAGACCGTCGATTCAGGGCACTGGCTCCCGACCACCTCTGACAACCACCGCCACTAAATTCACCGCCTG[C/T]
ATGCCTAGCCTCCATGACCAAGACACCGACCAACTAAGAAAGCAAAAAGGCCAACCTACGAGAGGACTCGACTATGGGGAGACCCATAGAATATCATAAC

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 94.90% 5.10% 0.02% 0.00% NA
All Indica  2759 91.40% 8.50% 0.04% 0.00% 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 90.60% 9.40% 0.00% 0.00% NA
Indica II  465 97.40% 2.60% 0.00% 0.00% NA
Indica III  913 90.80% 9.20% 0.00% 0.00% NA
Indica Intermediate  786 89.30% 10.60% 0.13% 0.00% NA
Temperate Japonica  767 99.60% 0.40% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 97.80% 2.20% 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
vg1200208711 G -> A LOC_Os12g01350.1 downstream_gene_variant ; 1520.0bp to feature; MODIFIER silent_mutation Average:82.357; most accessible tissue: Callus, score: 97.777 N N N N
vg1200208711 G -> A LOC_Os12g01355.1 downstream_gene_variant ; 1479.0bp to feature; MODIFIER silent_mutation Average:82.357; most accessible tissue: Callus, score: 97.777 N N N N
vg1200208711 G -> A LOC_Os12g01350-LOC_Os12g01355 intergenic_region ; MODIFIER silent_mutation Average:82.357; most accessible tissue: Callus, score: 97.777 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)
vg1200208711 G A -0.03 -0.03 -0.05 -0.03 -0.05 -0.05

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1200208711 NA 1.00E-12 Awn_length Ind_All YES Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652