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Detailed information for vg1009316722:

Variant ID: vg1009316722 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 9316722
Reference Allele: AAlternative Allele: T
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.97, T: 0.02, others allele: 0.00, population size: 119. )

Flanking Sequence (100 bp) in Reference Genome:


ACAACGTGGCTGCCCCTAGCCACGAATCCAACTAGAACTAGGACTCCTAATCACATAGGAAACCTACCAAACCAGGGAAACAACATCCCCATACAATTCC[A/T]
CGTTCCAATCTTTTCAAACTTGGACTCCAATCCAAATTTGACTACTCTTTCCATACGCACACAACACAACATGTATGTCATATGGAAACCTTCACCTCCA

Reverse complement sequence

TGGAGGTGAAGGTTTCCATATGACATACATGTTGTGTTGTGTGCGTATGGAAAGAGTAGTCAAATTTGGATTGGAGTCCAAGTTTGAAAAGATTGGAACG[T/A]
GGAATTGTATGGGGATGTTGTTTCCCTGGTTTGGTAGGTTTCCTATGTGATTAGGAGTCCTAGTTCTAGTTGGATTCGTGGCTAGGGGCAGCCACGTTGT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 60.80% 35.10% 1.84% 2.20% NA
All Indica  2759 43.70% 52.10% 2.03% 2.10% NA
All Japonica  1512 86.10% 13.40% 0.13% 0.33% NA
Aus  269 74.30% 0.00% 10.41% 15.24% NA
Indica I  595 27.70% 69.60% 1.18% 1.51% NA
Indica II  465 60.60% 36.60% 1.51% 1.29% NA
Indica III  913 39.80% 54.40% 2.30% 3.50% NA
Indica Intermediate  786 50.50% 45.40% 2.67% 1.40% NA
Temperate Japonica  767 94.50% 5.30% 0.13% 0.00% NA
Tropical Japonica  504 78.20% 20.60% 0.20% 0.99% NA
Japonica Intermediate  241 75.90% 24.10% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 77.80% 21.10% 1.11% 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
vg1009316722 A -> T LOC_Os10g18330.1 upstream_gene_variant ; 3662.0bp to feature; MODIFIER silent_mutation Average:67.649; most accessible tissue: Minghui63 young leaf, score: 86.015 N N N N
vg1009316722 A -> T LOC_Os10g18350.1 upstream_gene_variant ; 2444.0bp to feature; MODIFIER silent_mutation Average:67.649; most accessible tissue: Minghui63 young leaf, score: 86.015 N N N N
vg1009316722 A -> T LOC_Os10g18340.1 downstream_gene_variant ; 375.0bp to feature; MODIFIER silent_mutation Average:67.649; most accessible tissue: Minghui63 young leaf, score: 86.015 N N N N
vg1009316722 A -> T LOC_Os10g18340.2 downstream_gene_variant ; 379.0bp to feature; MODIFIER silent_mutation Average:67.649; most accessible tissue: Minghui63 young leaf, score: 86.015 N N N N
vg1009316722 A -> T LOC_Os10g18340-LOC_Os10g18350 intergenic_region ; MODIFIER silent_mutation Average:67.649; most accessible tissue: Minghui63 young leaf, score: 86.015 N N N N
vg1009316722 A -> DEL N N silent_mutation Average:67.649; most accessible tissue: Minghui63 young leaf, score: 86.015 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)
vg1009316722 A T -0.02 -0.03 0.0 0.0 -0.01 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1009316722 5.00E-06 NA mr1053 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
vg1009316722 1.08E-06 7.37E-07 mr1053 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
vg1009316722 1.24E-08 1.58E-10 mr1070 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
vg1009316722 1.28E-07 5.79E-07 mr1070 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
vg1009316722 3.11E-08 2.56E-11 mr1128 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
vg1009316722 7.02E-08 3.28E-08 mr1128 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
vg1009316722 5.37E-06 6.24E-06 mr1147 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
vg1009316722 NA 5.49E-07 mr1220 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
vg1009316722 NA 7.30E-06 mr1691 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
vg1009316722 NA 7.70E-10 mr1709 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
vg1009316722 NA 7.69E-11 mr1709 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
vg1009316722 NA 4.80E-09 mr1027_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
vg1009316722 6.58E-06 1.50E-06 mr1053_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
vg1009316722 4.35E-06 1.18E-06 mr1128_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
vg1009316722 NA 4.39E-06 mr1170_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
vg1009316722 NA 5.81E-06 mr1204_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
vg1009316722 NA 3.64E-09 mr1660_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
vg1009316722 NA 6.12E-07 mr1691_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
vg1009316722 NA 1.01E-13 mr1709_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
vg1009316722 NA 5.29E-11 mr1709_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