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Detailed information for vg0501354532:

Variant ID: vg0501354532 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 1354532
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 122. )

Flanking Sequence (100 bp) in Reference Genome:


CAGATCGAGTGGGTGCATAGCTGCAAAGGAGGGAGGGGGAGAGGAATCGCACCACCTAGGGTTTGGCCGTATGTGTTGGGCCGTGGCGTGCACGGATCGT[C/T]
GGCGGGGACGATGGCGGAGGAGAGGGAGAGAAGGGAGGGAAATCGTCACTGACCTTTGGCGGCCGGAGGGAGGGGGGGTGGGGGAATCGCCACTGACGAC

Reverse complement sequence

GTCGTCAGTGGCGATTCCCCCACCCCCCCTCCCTCCGGCCGCCAAAGGTCAGTGACGATTTCCCTCCCTTCTCTCCCTCTCCTCCGCCATCGTCCCCGCC[G/A]
ACGATCCGTGCACGCCACGGCCCAACACATACGGCCAAACCCTAGGTGGTGCGATTCCTCTCCCCCTCCCTCCTTTGCAGCTATGCACCCACTCGATCTG

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 69.00% 31.00% 0.04% 0.00% NA
All Indica  2759 54.50% 45.50% 0.04% 0.00% NA
All Japonica  1512 98.20% 1.70% 0.07% 0.00% NA
Aus  269 38.70% 61.30% 0.00% 0.00% NA
Indica I  595 73.80% 26.20% 0.00% 0.00% NA
Indica II  465 66.90% 33.10% 0.00% 0.00% NA
Indica III  913 33.40% 66.50% 0.11% 0.00% NA
Indica Intermediate  786 57.10% 42.90% 0.00% 0.00% NA
Temperate Japonica  767 97.30% 2.70% 0.00% 0.00% NA
Tropical Japonica  504 99.20% 0.60% 0.20% 0.00% NA
Japonica Intermediate  241 99.20% 0.80% 0.00% 0.00% NA
VI/Aromatic  96 97.90% 2.10% 0.00% 0.00% NA
Intermediate  90 80.00% 20.00% 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
vg0501354532 C -> T LOC_Os05g03330.1 downstream_gene_variant ; 4507.0bp to feature; MODIFIER silent_mutation Average:60.804; most accessible tissue: Zhenshan97 panicle, score: 95.806 N N N N
vg0501354532 C -> T LOC_Os05g03320.1 intron_variant ; MODIFIER silent_mutation Average:60.804; most accessible tissue: Zhenshan97 panicle, score: 95.806 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)
vg0501354532 C T -0.03 -0.05 -0.08 -0.05 -0.04 -0.05

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0501354532 NA 2.22E-10 mr1510 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
vg0501354532 NA 3.05E-07 mr1510 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
vg0501354532 NA 9.71E-06 mr1624 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
vg0501354532 NA 6.70E-06 mr1691 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