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Detailed information for vg0335727001:

Variant ID: vg0335727001 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 35727001
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 51. )

Flanking Sequence (100 bp) in Reference Genome:


CCAATTCACTCGAATCTTGTTGCTTGGCCACCGATGTTGTTTCTGTGCCATCAGTTGACAAATGCAGATGGAGACTGGACAATGAAGTAGTATATCTGCT[A/G]
GCTGCCTGTAGGGATATTTGTTGATTGCCTTCATGTATGTTTAAGACACTTAGTTTTGGTGCTTCAGGTAGAGTAGTCAGCTCTGGGCACTCGTTGATTG

Reverse complement sequence

CAATCAACGAGTGCCCAGAGCTGACTACTCTACCTGAAGCACCAAAACTAAGTGTCTTAAACATACATGAAGGCAATCAACAAATATCCCTACAGGCAGC[T/C]
AGCAGATATACTACTTCATTGTCCAGTCTCCATCTGCATTTGTCAACTGATGGCACAGAAACAACATCGGTGGCCAAGCAACAAGATTCGAGTGAATTGG

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 37.50% 6.00% 5.23% 51.29% NA
All Indica  2759 30.00% 9.60% 6.49% 53.86% NA
All Japonica  1512 52.60% 0.30% 1.98% 45.17% NA
Aus  269 40.10% 1.50% 10.78% 47.58% NA
Indica I  595 27.20% 3.50% 5.21% 64.03% NA
Indica II  465 19.80% 9.20% 9.25% 61.72% NA
Indica III  913 40.10% 12.20% 4.38% 43.37% NA
Indica Intermediate  786 26.50% 11.60% 8.27% 53.69% NA
Temperate Japonica  767 87.10% 0.00% 0.78% 12.13% NA
Tropical Japonica  504 7.70% 0.80% 3.17% 88.29% NA
Japonica Intermediate  241 36.50% 0.00% 3.32% 60.17% NA
VI/Aromatic  96 6.20% 1.00% 6.25% 86.46% NA
Intermediate  90 40.00% 7.80% 3.33% 48.89% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0335727001 A -> DEL LOC_Os03g63220.1 N frameshift_variant Average:43.941; most accessible tissue: Callus, score: 87.728 N N N N
vg0335727001 A -> G LOC_Os03g63220.1 synonymous_variant ; p.Ala65Ala; LOW synonymous_codon Average:43.941; most accessible tissue: Callus, score: 87.728 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)
vg0335727001 A G 0.0 0.0 0.01 0.0 0.0 -0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0335727001 NA 4.30E-06 mr1069 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
vg0335727001 NA 5.72E-06 mr1149 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
vg0335727001 NA 6.27E-13 mr1180 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
vg0335727001 NA 3.21E-09 mr1180 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
vg0335727001 NA 2.22E-14 mr1183 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
vg0335727001 NA 1.06E-07 mr1183 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
vg0335727001 NA 5.56E-14 mr1503 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
vg0335727001 NA 1.90E-07 mr1503 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
vg0335727001 NA 7.81E-09 mr1918 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
vg0335727001 NA 8.37E-12 mr1929 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
vg0335727001 NA 1.67E-06 mr1929 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
vg0335727001 NA 9.02E-07 mr1099_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
vg0335727001 NA 1.11E-06 mr1180_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
vg0335727001 1.99E-06 NA mr1222_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
vg0335727001 1.74E-06 4.34E-08 mr1222_2 Ind_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
vg0335727001 NA 1.39E-07 mr1929_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