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Detailed information for vg0604919053:

Variant ID: vg0604919053 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 4919053
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.56, C: 0.44, others allele: 0.00, population size: 94. )

Flanking Sequence (100 bp) in Reference Genome:


ACAAAGGCCAGGGGGTGAGAGATGACGACGCGGTTGTGGCCTCGGCACCTCGGCTTGCGTCGGGCGTCGGTCGTGGCCTCCGTGCGCGCGGCGAGGACAG[T/C]
GGCGTCGTGTGCGCGCGCCAGCTAGCTTCCCCCAGCCACGACCCACGGGATGGCGACGCGTGGGCCTGTACTACGTGCAGCGGCGTGAGGATGGCGTGCG

Reverse complement sequence

CGCACGCCATCCTCACGCCGCTGCACGTAGTACAGGCCCACGCGTCGCCATCCCGTGGGTCGTGGCTGGGGGAAGCTAGCTGGCGCGCGCACACGACGCC[A/G]
CTGTCCTCGCCGCGCGCACGGAGGCCACGACCGACGCCCGACGCAAGCCGAGGTGCCGAGGCCACAACCGCGTCGTCATCTCTCACCCCCTGGCCTTTGT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 42.80% 36.60% 0.85% 19.81% NA
All Indica  2759 19.50% 57.70% 0.54% 22.22% NA
All Japonica  1512 81.70% 5.80% 0.73% 11.84% NA
Aus  269 50.60% 7.10% 0.74% 41.64% NA
Indica I  595 21.50% 64.20% 0.34% 13.95% NA
Indica II  465 31.80% 28.20% 0.86% 39.14% NA
Indica III  913 9.10% 74.20% 0.77% 15.99% NA
Indica Intermediate  786 22.90% 51.10% 0.25% 25.70% NA
Temperate Japonica  767 93.40% 2.20% 0.78% 3.65% NA
Tropical Japonica  504 65.50% 11.10% 0.60% 22.82% NA
Japonica Intermediate  241 78.40% 5.80% 0.83% 14.94% NA
VI/Aromatic  96 71.90% 2.10% 8.33% 17.71% NA
Intermediate  90 46.70% 32.20% 4.44% 16.67% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0604919053 T -> C LOC_Os06g09650-LOC_Os06g09660 intergenic_region ; MODIFIER silent_mutation Average:96.784; most accessible tissue: Callus, score: 98.906 N N N N
vg0604919053 T -> DEL N N silent_mutation Average:96.784; most accessible tissue: Callus, score: 98.906 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)
vg0604919053 T C 0.05 0.05 0.04 0.01 0.03 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0604919053 NA 2.44E-09 mr1059 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
vg0604919053 NA 2.17E-15 mr1143 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
vg0604919053 NA 2.61E-11 mr1143 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
vg0604919053 NA 1.20E-09 mr1167 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
vg0604919053 NA 2.78E-06 mr1201 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
vg0604919053 NA 4.48E-08 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
vg0604919053 NA 1.12E-08 mr1399 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
vg0604919053 NA 1.32E-09 mr1535 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
vg0604919053 NA 9.75E-11 mr1675 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
vg0604919053 NA 3.23E-09 mr1726 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
vg0604919053 NA 3.43E-10 mr1969 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
vg0604919053 NA 1.04E-16 mr1995 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
vg0604919053 NA 2.72E-13 mr1995 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
vg0604919053 NA 7.99E-06 mr1201_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
vg0604919053 NA 1.73E-07 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
vg0604919053 NA 2.40E-07 mr1830_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