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Detailed information for vg0621172424:

Variant ID: vg0621172424 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 21172424
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 295. )

Flanking Sequence (100 bp) in Reference Genome:


CCGTGTTTGCACTGGTTTTAGAAGGACATGATTCAAACTCGACGTCAAGATGAGGGAGCTGAAATGAACTTATTCGTAGTTATTGCCCATGTAAAATTAG[C/A]
GGTAGGCTTAATCTCGGCCTGTTGTTTGCCCAATTTTGTTTTTTTAAGAGCATCCTCAGCAGCTCATCCATATTCGATCCTCCATATGCCTATTTAGATG

Reverse complement sequence

CATCTAAATAGGCATATGGAGGATCGAATATGGATGAGCTGCTGAGGATGCTCTTAAAAAAACAAAATTGGGCAAACAACAGGCCGAGATTAAGCCTACC[G/T]
CTAATTTTACATGGGCAATAACTACGAATAAGTTCATTTCAGCTCCCTCATCTTGACGTCGAGTTTGAATCATGTCCTTCTAAAACCAGTGCAAACACGG

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 93.10% 5.60% 1.31% 0.00% NA
All Indica  2759 99.80% 0.10% 0.07% 0.00% NA
All Japonica  1512 79.20% 17.00% 3.84% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.80% 0.00% 0.22% 0.00% NA
Indica III  913 99.80% 0.20% 0.00% 0.00% NA
Indica Intermediate  786 99.70% 0.10% 0.13% 0.00% NA
Temperate Japonica  767 88.50% 8.10% 3.39% 0.00% NA
Tropical Japonica  504 72.80% 24.60% 2.58% 0.00% NA
Japonica Intermediate  241 62.70% 29.50% 7.88% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 92.20% 5.60% 2.22% 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
vg0621172424 C -> A LOC_Os06g36170.1 upstream_gene_variant ; 876.0bp to feature; MODIFIER silent_mutation Average:84.412; most accessible tissue: Zhenshan97 flag leaf, score: 87.087 N N N N
vg0621172424 C -> A LOC_Os06g36170-LOC_Os06g36180 intergenic_region ; MODIFIER silent_mutation Average:84.412; most accessible tissue: Zhenshan97 flag leaf, score: 87.087 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)
vg0621172424 C A -0.05 -0.03 -0.05 -0.03 -0.05 -0.06

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0621172424 5.34E-08 NA mr1238 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
vg0621172424 5.36E-06 NA mr1309 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
vg0621172424 3.13E-07 9.93E-16 mr1484 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
vg0621172424 4.44E-10 NA mr1238_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
vg0621172424 NA 1.79E-06 mr1238_2 Jap_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
vg0621172424 6.53E-10 NA mr1484_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
vg0621172424 6.94E-06 6.94E-06 mr1484_2 Jap_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
vg0621172424 1.17E-08 NA mr1841_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
vg0621172424 NA 1.72E-06 mr1841_2 Jap_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
vg0621172424 3.27E-08 NA mr1900_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
vg0621172424 NA 2.06E-06 mr1900_2 Jap_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
vg0621172424 5.50E-08 NA mr1945_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