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Detailed information for vg0605306584:

Variant ID: vg0605306584 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 5306584
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.96, T: 0.04, others allele: 0.00, population size: 99. )

Flanking Sequence (100 bp) in Reference Genome:


GCCGTGCTCCCCTTCTCCCGTGTCGCCGTGTTTCCCAGCTGCAGCTGCCGCCGCCGGGCGCCGGCCGCCGTCGTGTTGCTGGCCACCGTCGCGGCGCCGC[C/T]
GCTCTCCTCTCTCCCGCCTCGCCTGCCGGCCTCCCGCCGCTTGCCTCGCCCAGAAAGAGAGACGAGGAGAAAGAGGAGGGTGATGACGTAGATTACGCTG

Reverse complement sequence

CAGCGTAATCTACGTCATCACCCTCCTCTTTCTCCTCGTCTCTCTTTCTGGGCGAGGCAAGCGGCGGGAGGCCGGCAGGCGAGGCGGGAGAGAGGAGAGC[G/A]
GCGGCGCCGCGACGGTGGCCAGCAACACGACGGCGGCCGGCGCCCGGCGGCGGCAGCTGCAGCTGGGAAACACGGCGACACGGGAGAAGGGGAGCACGGC

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 53.50% 44.50% 1.97% 0.00% NA
All Indica  2759 27.80% 69.90% 2.25% 0.00% NA
All Japonica  1512 90.50% 8.00% 1.52% 0.00% NA
Aus  269 94.40% 4.80% 0.74% 0.00% NA
Indica I  595 37.10% 58.20% 4.71% 0.00% NA
Indica II  465 5.20% 92.50% 2.37% 0.00% NA
Indica III  913 34.70% 65.00% 0.33% 0.00% NA
Indica Intermediate  786 26.20% 71.20% 2.54% 0.00% NA
Temperate Japonica  767 97.00% 1.30% 1.69% 0.00% NA
Tropical Japonica  504 78.80% 19.60% 1.59% 0.00% NA
Japonica Intermediate  241 94.20% 5.00% 0.83% 0.00% NA
VI/Aromatic  96 90.60% 9.40% 0.00% 0.00% NA
Intermediate  90 58.90% 34.40% 6.67% 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
vg0605306584 C -> T LOC_Os06g10320.1 synonymous_variant ; p.Ala167Ala; LOW synonymous_codon Average:72.99; most accessible tissue: Minghui63 panicle, score: 92.666 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)
vg0605306584 C T -0.06 -0.05 -0.03 -0.05 -0.04 -0.04

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0605306584 4.09E-21 1.06E-19 mr1201 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
vg0605306584 4.86E-24 1.12E-46 mr1201 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
vg0605306584 7.42E-17 3.37E-16 mr1219 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
vg0605306584 7.87E-21 2.21E-40 mr1219 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
vg0605306584 8.00E-16 5.34E-12 mr1274 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
vg0605306584 1.36E-22 2.50E-40 mr1274 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
vg0605306584 6.10E-15 4.02E-15 mr1201_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
vg0605306584 1.09E-21 1.37E-39 mr1201_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
vg0605306584 8.69E-14 8.60E-16 mr1219_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
vg0605306584 8.60E-18 1.58E-35 mr1219_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
vg0605306584 2.45E-12 3.63E-13 mr1274_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
vg0605306584 2.82E-17 2.76E-36 mr1274_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