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Detailed information for vg1001831505:

Variant ID: vg1001831505 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 1831505
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.97, A: 0.04, others allele: 0.00, population size: 236. )

Flanking Sequence (100 bp) in Reference Genome:


TTCTCGCTTGCTATCCCCTCTCTTTAATTTATCTCTTTCTAACATATATACTCTAACTCCCAAGGACTCGAGCCAGTTGTTGCCTCCTTGATCCGTCCTC[G/A]
AACTCCAGCCATCATCGCCTCTGGCCCCGAAAACGAGCCGCCACCACCATCTTCACCCCCTAACCCCAAGCACCGGCCACCACCTTAGAGATGCCAGATC

Reverse complement sequence

GATCTGGCATCTCTAAGGTGGTGGCCGGTGCTTGGGGTTAGGGGGTGAAGATGGTGGTGGCGGCTCGTTTTCGGGGCCAGAGGCGATGATGGCTGGAGTT[C/T]
GAGGACGGATCAAGGAGGCAACAACTGGCTCGAGTCCTTGGGAGTTAGAGTATATATGTTAGAAAGAGATAAATTAAAGAGAGGGGATAGCAAGCGAGAA

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 64.30% 35.60% 0.13% 0.00% NA
All Indica  2759 40.60% 59.30% 0.14% 0.00% NA
All Japonica  1512 98.10% 1.70% 0.13% 0.00% NA
Aus  269 99.30% 0.70% 0.00% 0.00% NA
Indica I  595 45.70% 54.10% 0.17% 0.00% NA
Indica II  465 32.00% 67.70% 0.22% 0.00% NA
Indica III  913 40.90% 59.10% 0.00% 0.00% NA
Indica Intermediate  786 41.30% 58.40% 0.25% 0.00% NA
Temperate Japonica  767 99.30% 0.70% 0.00% 0.00% NA
Tropical Japonica  504 96.20% 3.60% 0.20% 0.00% NA
Japonica Intermediate  241 98.30% 1.20% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 81.10% 18.90% 0.00% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1001831505 G -> A LOC_Os10g04000.1 upstream_gene_variant ; 1128.0bp to feature; MODIFIER silent_mutation Average:72.662; most accessible tissue: Zhenshan97 root, score: 92.495 N N N N
vg1001831505 G -> A LOC_Os10g04010.1 downstream_gene_variant ; 1699.0bp to feature; MODIFIER silent_mutation Average:72.662; most accessible tissue: Zhenshan97 root, score: 92.495 N N N N
vg1001831505 G -> A LOC_Os10g04000-LOC_Os10g04010 intergenic_region ; MODIFIER silent_mutation Average:72.662; most accessible tissue: Zhenshan97 root, score: 92.495 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)
vg1001831505 G A 0.02 0.0 0.0 0.0 0.01 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1001831505 7.57E-10 NA mr1486 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
vg1001831505 3.27E-10 7.89E-14 mr1486 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
vg1001831505 2.69E-07 NA mr1548 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
vg1001831505 2.14E-07 1.82E-09 mr1548 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
vg1001831505 NA 5.21E-07 mr1588 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
vg1001831505 9.03E-08 NA mr1486_2 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
vg1001831505 2.34E-08 9.98E-12 mr1486_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
vg1001831505 NA 6.08E-06 mr1588_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
vg1001831505 NA 6.20E-07 mr1721_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