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Detailed information for vg0429988139:

Variant ID: vg0429988139 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 29988139
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.02, others allele: 0.00, population size: 120. )

Flanking Sequence (100 bp) in Reference Genome:


CGGTCGCAGCGGTAGTTCTTCTTGAGGCCCTGCGACGAAGCCATCGCGAGGCGGCGGGAGGGAACGACGGCGGCGGAGGCTAGGGTTTTGCTGCGGCGGC[G/A]
GCGGCGGCGCGAGACAGAGGATGGGTTTAAGCTAGGTGGCGGGTGTAAATGGGAAAGGGTGTCCCCGACATGTGGGCCCTATCTTGTAGGCTGACATGTG

Reverse complement sequence

CACATGTCAGCCTACAAGATAGGGCCCACATGTCGGGGACACCCTTTCCCATTTACACCCGCCACCTAGCTTAAACCCATCCTCTGTCTCGCGCCGCCGC[C/T]
GCCGCCGCAGCAAAACCCTAGCCTCCGCCGCCGTCGTTCCCTCCCGCCGCCTCGCGATGGCTTCGTCGCAGGGCCTCAAGAAGAACTACCGCTGCGACCG

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 83.70% 15.90% 0.00% 0.42% NA
All Indica  2759 72.70% 26.70% 0.00% 0.65% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.07% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 81.20% 18.80% 0.00% 0.00% NA
Indica II  465 34.20% 64.70% 0.00% 1.08% NA
Indica III  913 83.50% 16.10% 0.00% 0.44% NA
Indica Intermediate  786 76.50% 22.40% 0.00% 1.15% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.20% 0.40% 0.00% 0.41% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 82.20% 16.70% 0.00% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0429988139 G -> DEL N N silent_mutation Average:99.279; most accessible tissue: Minghui63 young leaf, score: 99.677 N N N N
vg0429988139 G -> A LOC_Os04g50660.1 5_prime_UTR_premature_start_codon_gain_variant ; LOW silent_mutation Average:99.279; most accessible tissue: Minghui63 young leaf, score: 99.677 N N N N
vg0429988139 G -> A LOC_Os04g50660.1 5_prime_UTR_variant ; 57.0bp to feature; MODIFIER silent_mutation Average:99.279; most accessible tissue: Minghui63 young leaf, score: 99.677 N N N N
vg0429988139 G -> A LOC_Os04g50670.1 downstream_gene_variant ; 1027.0bp to feature; MODIFIER silent_mutation Average:99.279; most accessible tissue: Minghui63 young leaf, score: 99.677 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)
vg0429988139 G A -0.03 -0.05 -0.05 -0.04 -0.03 -0.04

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0429988139 NA 3.20E-13 mr1138 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
vg0429988139 NA 9.25E-08 mr1138 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
vg0429988139 1.82E-07 1.06E-22 mr1169 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
vg0429988139 1.20E-06 3.85E-14 mr1169 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
vg0429988139 3.23E-13 1.86E-28 mr1174 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
vg0429988139 9.93E-16 3.75E-27 mr1174 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
vg0429988139 3.42E-10 2.91E-15 mr1347 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
vg0429988139 2.87E-10 2.73E-16 mr1347 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
vg0429988139 NA 2.06E-09 mr1354 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
vg0429988139 NA 2.00E-09 mr1354 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
vg0429988139 7.29E-09 9.84E-08 mr1406 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
vg0429988139 4.11E-09 1.99E-11 mr1406 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
vg0429988139 NA 1.98E-14 mr1138_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
vg0429988139 NA 3.74E-08 mr1138_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
vg0429988139 1.93E-12 2.23E-29 mr1174_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
vg0429988139 6.40E-16 4.46E-29 mr1174_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
vg0429988139 3.04E-14 1.79E-24 mr1347_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
vg0429988139 5.40E-15 9.33E-27 mr1347_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
vg0429988139 NA 9.45E-11 mr1354_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
vg0429988139 NA 2.22E-11 mr1354_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
vg0429988139 5.42E-07 9.56E-08 mr1406_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
vg0429988139 1.44E-07 2.89E-10 mr1406_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
vg0429988139 NA 1.26E-06 mr1540_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
vg0429988139 NA 9.21E-07 mr1732_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