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Detailed information for vg0524587148:

Variant ID: vg0524587148 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 24587148
Reference Allele: GAlternative Allele: T
Primary Allele: TSecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, T: 0.01, others allele: 0.00, population size: 108. )

Flanking Sequence (100 bp) in Reference Genome:


CACTGCACTCCGGCGCGCGCACCAACCAACCAACCAACCAACCAACCAACCAACCAAGCCTCCCAACTCCATGAGCAAGTTGCAGCAGCCGCAGGCCACA[G/T]
GCTCGAGCTTACTAGCTAGGCGGAGTAGAGTCCGTCGCACTCAACGCTCTGTTTCACACACGCACGCACCCATCTGAAAGCACGGCGCGACCAAACGCAT

Reverse complement sequence

ATGCGTTTGGTCGCGCCGTGCTTTCAGATGGGTGCGTGCGTGTGTGAAACAGAGCGTTGAGTGCGACGGACTCTACTCCGCCTAGCTAGTAAGCTCGAGC[C/A]
TGTGGCCTGCGGCTGCTGCAACTTGCTCATGGAGTTGGGAGGCTTGGTTGGTTGGTTGGTTGGTTGGTTGGTTGGTTGGTGCGCGCGCCGGAGTGCAGTG

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 55.80% 43.80% 0.28% 0.19% NA
All Indica  2759 91.30% 8.30% 0.29% 0.14% NA
All Japonica  1512 0.50% 99.10% 0.13% 0.26% NA
Aus  269 23.80% 75.80% 0.37% 0.00% NA
Indica I  595 96.60% 2.90% 0.00% 0.50% NA
Indica II  465 68.20% 31.60% 0.22% 0.00% NA
Indica III  913 99.00% 0.90% 0.11% 0.00% NA
Indica Intermediate  786 91.90% 7.30% 0.76% 0.13% NA
Temperate Japonica  767 0.00% 99.90% 0.00% 0.13% NA
Tropical Japonica  504 1.60% 98.00% 0.20% 0.20% NA
Japonica Intermediate  241 0.00% 98.80% 0.41% 0.83% NA
VI/Aromatic  96 2.10% 97.90% 0.00% 0.00% NA
Intermediate  90 48.90% 47.80% 2.22% 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
vg0524587148 G -> T LOC_Os05g42000.1 5_prime_UTR_premature_start_codon_gain_variant ; LOW silent_mutation Average:96.626; most accessible tissue: Zhenshan97 young leaf, score: 99.105 N N N N
vg0524587148 G -> T LOC_Os05g42000.2 5_prime_UTR_premature_start_codon_gain_variant ; LOW silent_mutation Average:96.626; most accessible tissue: Zhenshan97 young leaf, score: 99.105 N N N N
vg0524587148 G -> T LOC_Os05g42000.1 5_prime_UTR_variant ; 269.0bp to feature; MODIFIER silent_mutation Average:96.626; most accessible tissue: Zhenshan97 young leaf, score: 99.105 N N N N
vg0524587148 G -> T LOC_Os05g42000.2 5_prime_UTR_variant ; 269.0bp to feature; MODIFIER silent_mutation Average:96.626; most accessible tissue: Zhenshan97 young leaf, score: 99.105 N N N N
vg0524587148 G -> T LOC_Os05g41990.1 downstream_gene_variant ; 2203.0bp to feature; MODIFIER silent_mutation Average:96.626; most accessible tissue: Zhenshan97 young leaf, score: 99.105 N N N N
vg0524587148 G -> T LOC_Os05g42010.1 downstream_gene_variant ; 1176.0bp to feature; MODIFIER silent_mutation Average:96.626; most accessible tissue: Zhenshan97 young leaf, score: 99.105 N N N N
vg0524587148 G -> T LOC_Os05g42010.2 downstream_gene_variant ; 1176.0bp to feature; MODIFIER silent_mutation Average:96.626; most accessible tissue: Zhenshan97 young leaf, score: 99.105 N N N N
vg0524587148 G -> DEL N N silent_mutation Average:96.626; most accessible tissue: Zhenshan97 young leaf, score: 99.105 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)
vg0524587148 G T 0.06 -0.01 -0.13 -0.07 0.0 0.06

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0524587148 NA 1.89E-21 mr1020 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
vg0524587148 NA 1.62E-16 mr1032 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
vg0524587148 NA 6.60E-06 mr1032 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
vg0524587148 NA 1.45E-16 mr1165 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
vg0524587148 NA 6.60E-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
vg0524587148 NA 3.95E-16 mr1478 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
vg0524587148 NA 1.00E-06 mr1796 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
vg0524587148 8.32E-10 2.76E-58 mr1889 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
vg0524587148 3.07E-16 5.70E-32 mr1889 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
vg0524587148 7.16E-10 1.78E-68 mr1896 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
vg0524587148 2.99E-16 1.95E-30 mr1896 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
vg0524587148 3.52E-13 3.52E-30 mr1903 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
vg0524587148 1.72E-18 1.82E-32 mr1903 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
vg0524587148 5.58E-15 2.01E-88 mr1907 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
vg0524587148 2.25E-23 3.38E-48 mr1907 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
vg0524587148 1.20E-14 NA mr1934 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
vg0524587148 1.71E-20 6.68E-39 mr1934 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
vg0524587148 6.05E-10 NA mr1935 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
vg0524587148 1.00E-14 3.28E-28 mr1935 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
vg0524587148 NA 2.56E-57 mr1109_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
vg0524587148 NA 5.27E-06 mr1332_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
vg0524587148 NA 2.85E-06 mr1428_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
vg0524587148 NA 1.66E-08 mr1478_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
vg0524587148 NA 4.26E-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
vg0524587148 9.35E-06 7.43E-11 mr1612_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
vg0524587148 NA 1.01E-10 mr1715_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
vg0524587148 1.70E-07 6.67E-69 mr1889_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
vg0524587148 2.02E-10 7.19E-26 mr1889_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
vg0524587148 4.52E-09 7.30E-67 mr1896_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
vg0524587148 3.54E-13 4.26E-25 mr1896_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
vg0524587148 9.30E-13 2.19E-95 mr1907_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
vg0524587148 3.58E-16 5.45E-36 mr1907_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
vg0524587148 2.36E-12 NA mr1934_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
vg0524587148 6.78E-17 9.78E-35 mr1934_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