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Detailed information for vg0502009146:

Variant ID: vg0502009146 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 2009146
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.95, C: 0.05, others allele: 0.00, population size: 107. )

Flanking Sequence (100 bp) in Reference Genome:


GGCGCACATGTATACAAGTAATTCGATAATTATTGTTGTACATAAATAAATCATACTCCCTTTGTTCTTAATATTTACACTTGTCTTGTAAATTGTACAG[T/C]
TTTTTTTTAATGAAGTGAGCGTATCTCAACTGGTTAGATTCCTTGTGGTGGAATCAATCTACTTGGATTTAAATTATAAATTTAACACGGGTGCTTCCTT

Reverse complement sequence

AAGGAAGCACCCGTGTTAAATTTATAATTTAAATCCAAGTAGATTGATTCCACCACAAGGAATCTAACCAGTTGAGATACGCTCACTTCATTAAAAAAAA[A/G]
CTGTACAATTTACAAGACAAGTGTAAATATTAAGAACAAAGGGAGTATGATTTATTTATGTACAACAATAATTATCGAATTACTTGTATACATGTGCGCC

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 49.30% 40.00% 1.59% 9.08% NA
All Indica  2759 77.00% 21.90% 0.29% 0.80% NA
All Japonica  1512 7.40% 81.00% 1.26% 10.32% NA
Aus  269 22.70% 2.20% 4.83% 70.26% NA
Indica I  595 99.20% 0.80% 0.00% 0.00% NA
Indica II  465 79.40% 17.60% 0.43% 2.58% NA
Indica III  913 57.40% 42.20% 0.33% 0.11% NA
Indica Intermediate  786 81.60% 16.90% 0.38% 1.15% NA
Temperate Japonica  767 1.60% 96.10% 0.52% 1.83% NA
Tropical Japonica  504 11.30% 61.70% 2.78% 24.21% NA
Japonica Intermediate  241 17.80% 73.40% 0.41% 8.30% NA
VI/Aromatic  96 2.10% 5.20% 35.42% 57.29% NA
Intermediate  90 34.40% 56.70% 1.11% 7.78% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0502009146 T -> DEL N N silent_mutation Average:41.982; most accessible tissue: Zhenshan97 flower, score: 91.994 N N N N
vg0502009146 T -> C LOC_Os05g04380.1 upstream_gene_variant ; 969.0bp to feature; MODIFIER silent_mutation Average:41.982; most accessible tissue: Zhenshan97 flower, score: 91.994 N N N N
vg0502009146 T -> C LOC_Os05g04380.2 upstream_gene_variant ; 969.0bp to feature; MODIFIER silent_mutation Average:41.982; most accessible tissue: Zhenshan97 flower, score: 91.994 N N N N
vg0502009146 T -> C LOC_Os05g04370-LOC_Os05g04380 intergenic_region ; MODIFIER silent_mutation Average:41.982; most accessible tissue: Zhenshan97 flower, score: 91.994 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)
vg0502009146 T C 0.02 0.02 0.03 0.0 0.0 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0502009146 NA 2.40E-06 mr1114 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
vg0502009146 NA 1.75E-06 mr1119 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
vg0502009146 NA 1.39E-06 mr1120 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
vg0502009146 NA 5.34E-06 mr1189 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
vg0502009146 NA 5.94E-06 mr1782 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
vg0502009146 8.94E-06 NA mr1030_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
vg0502009146 9.81E-06 4.47E-06 mr1030_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
vg0502009146 1.44E-06 8.22E-09 mr1113_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
vg0502009146 NA 1.66E-07 mr1114_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
vg0502009146 4.40E-06 2.62E-07 mr1117_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
vg0502009146 NA 2.73E-06 mr1119_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
vg0502009146 5.82E-07 4.52E-09 mr1120_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
vg0502009146 NA 8.33E-13 mr1147_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
vg0502009146 4.58E-08 2.29E-09 mr1247_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
vg0502009146 NA 9.60E-06 mr1258_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
vg0502009146 NA 2.12E-06 mr1358_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
vg0502009146 NA 8.72E-07 mr1754_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
vg0502009146 NA 8.88E-10 mr1946_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
vg0502009146 NA 8.88E-10 mr1948_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