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Detailed information for vg1126224167:

Variant ID: vg1126224167 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 26224167
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.67, A: 0.33, others allele: 0.00, population size: 85. )

Flanking Sequence (100 bp) in Reference Genome:


GATGATAAATCAAGTTATAATAAAATAAATGATAATTATATTTTTAATAAAACGAATGAAAAAACGTATAAAAAATCAACAGTATTATATATTAAAAAAA[G/A]
GATGGAGTAGTACTTGCTATGTGTGTCCTGACATAATAACACACGATTGATGACCCCTCTTAATTAGTCCATATACCCGCAATAGTTTTAAAATTTATCC

Reverse complement sequence

GGATAAATTTTAAAACTATTGCGGGTATATGGACTAATTAAGAGGGGTCATCAATCGTGTGTTATTATGTCAGGACACACATAGCAAGTACTACTCCATC[C/T]
TTTTTTTAATATATAATACTGTTGATTTTTTATACGTTTTTTCATTCGTTTTATTAAAAATATAATTATCATTTATTTTATTATAACTTGATTTATCATC

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 44.30% 37.80% 0.47% 17.48% NA
All Indica  2759 32.30% 52.20% 0.54% 14.93% NA
All Japonica  1512 70.40% 3.60% 0.20% 25.79% NA
Aus  269 30.50% 67.70% 0.00% 1.86% NA
Indica I  595 11.40% 53.10% 0.50% 34.96% NA
Indica II  465 23.40% 59.10% 0.00% 17.42% NA
Indica III  913 42.90% 49.20% 0.00% 7.89% NA
Indica Intermediate  786 41.00% 51.00% 1.53% 6.49% NA
Temperate Japonica  767 94.50% 1.60% 0.39% 3.52% NA
Tropical Japonica  504 37.70% 4.00% 0.00% 58.33% NA
Japonica Intermediate  241 62.20% 9.10% 0.00% 28.63% NA
VI/Aromatic  96 20.80% 78.10% 1.04% 0.00% NA
Intermediate  90 38.90% 36.70% 3.33% 21.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1126224167 G -> A LOC_Os11g43420.1 downstream_gene_variant ; 3414.0bp to feature; MODIFIER silent_mutation Average:49.777; most accessible tissue: Minghui63 root, score: 96.57 N N N N
vg1126224167 G -> A LOC_Os11g43430.1 downstream_gene_variant ; 1424.0bp to feature; MODIFIER silent_mutation Average:49.777; most accessible tissue: Minghui63 root, score: 96.57 N N N N
vg1126224167 G -> A LOC_Os11g43420-LOC_Os11g43430 intergenic_region ; MODIFIER silent_mutation Average:49.777; most accessible tissue: Minghui63 root, score: 96.57 N N N N
vg1126224167 G -> DEL N N silent_mutation Average:49.777; most accessible tissue: Minghui63 root, score: 96.57 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)
vg1126224167 G A -0.08 -0.09 -0.06 -0.04 -0.07 -0.05

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1126224167 8.30E-06 2.39E-08 mr1133 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
vg1126224167 NA 9.10E-06 mr1644 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
vg1126224167 3.04E-06 1.65E-08 mr1667 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
vg1126224167 NA 2.71E-07 mr1133_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
vg1126224167 NA 8.47E-07 mr1667_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