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Detailed information for vg0527361614:

Variant ID: vg0527361614 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 27361614
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GCAGGCGAGACGGAGTGGTTGGGGCTGTGCAAGGAGGTGGTGATGGTGCCCGTGCTCAAGGATTGGCTCATGAACGAGAAGTACTACGGCAAATTGGGCG[A/G]
CGATGGATACGGCGCCGTGCTGAAGCGCGGGTTCCAGCTGAGCTGGGACCCGACGGCGGGGATGTGCCACGAGTGCGAGGTATCCGGGGGACGCTGCAGC

Reverse complement sequence

GCTGCAGCGTCCCCCGGATACCTCGCACTCGTGGCACATCCCCGCCGTCGGGTCCCAGCTCAGCTGGAACCCGCGCTTCAGCACGGCGCCGTATCCATCG[T/C]
CGCCCAATTTGCCGTAGTACTTCTCGTTCATGAGCCAATCCTTGAGCACGGGCACCATCACCACCTCCTTGCACAGCCCCAACCACTCCGTCTCGCCTGC

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 88.90% 5.20% 2.69% 3.24% NA
All Indica  2759 92.60% 3.80% 1.74% 1.88% NA
All Japonica  1512 80.40% 8.40% 4.89% 6.28% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 99.20% 0.70% 0.17% 0.00% NA
Indica II  465 68.00% 15.70% 7.53% 8.82% NA
Indica III  913 99.80% 0.20% 0.00% 0.00% NA
Indica Intermediate  786 93.80% 3.30% 1.53% 1.40% NA
Temperate Japonica  767 99.00% 0.50% 0.26% 0.26% NA
Tropical Japonica  504 57.50% 17.50% 10.71% 14.29% NA
Japonica Intermediate  241 69.30% 14.50% 7.47% 8.71% NA
VI/Aromatic  96 88.50% 3.10% 3.12% 5.21% NA
Intermediate  90 85.60% 11.10% 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
vg0527361614 A -> DEL LOC_Os05g47770.1 N frameshift_variant Average:64.671; most accessible tissue: Zhenshan97 root, score: 91.073 N N N N
vg0527361614 A -> G LOC_Os05g47770.1 missense_variant ; p.Asp222Gly; MODERATE nonsynonymous_codon ; D222G Average:64.671; most accessible tissue: Zhenshan97 root, score: 91.073 benign 0.181 TOLERATED 0.54

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)
vg0527361614 A G 0.02 0.03 0.03 0.02 0.02 0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0527361614 NA 5.85E-12 mr1079 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
vg0527361614 NA 9.94E-12 mr1178 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
vg0527361614 NA 3.65E-12 mr1390 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
vg0527361614 NA 2.03E-11 mr1490 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
vg0527361614 NA 4.45E-06 mr1156_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
vg0527361614 NA 5.51E-08 mr1158_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
vg0527361614 NA 2.60E-06 mr1175_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
vg0527361614 NA 9.85E-06 mr1186_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
vg0527361614 NA 1.05E-07 mr1193_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
vg0527361614 NA 1.77E-14 mr1195_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
vg0527361614 NA 5.26E-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
vg0527361614 NA 1.43E-10 mr1352_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
vg0527361614 NA 2.40E-07 mr1383_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
vg0527361614 NA 4.52E-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
vg0527361614 NA 2.26E-06 mr1482_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
vg0527361614 NA 1.42E-09 mr1546_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
vg0527361614 NA 7.43E-06 mr1580_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
vg0527361614 NA 5.26E-08 mr1645_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
vg0527361614 NA 6.78E-09 mr1682_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
vg0527361614 NA 9.90E-06 mr1756_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
vg0527361614 NA 2.10E-07 mr1798_2 Jap_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
vg0527361614 NA 4.63E-08 mr1828_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