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Detailed information for vg1019539225:

Variant ID: vg1019539225 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 19539225
Reference Allele: TAlternative Allele: G
Primary Allele: TSecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.87, T: 0.13, others allele: 0.00, population size: 86. )

Flanking Sequence (100 bp) in Reference Genome:


CTGGTCCTGCACAGTGTTTCCCGAAGATATTTCCGTTTGCTTTCTGCACAGTTGGAACATGCATACTCCCTCCCTCCAAAAAAAAAAAGAAAAACTCTTA[T/G]
TTTTTTGTCCAACGTTTGACCGTATGTCTTATTTGAAAAAATTAAAAAGACAAGTCACGTATAAAGTATTAATCATGTTTTATCATCTAATAACAATGAA

Reverse complement sequence

TTCATTGTTATTAGATGATAAAACATGATTAATACTTTATACGTGACTTGTCTTTTTAATTTTTTCAAATAAGACATACGGTCAAACGTTGGACAAAAAA[A/C]
TAAGAGTTTTTCTTTTTTTTTTTGGAGGGAGGGAGTATGCATGTTCCAACTGTGCAGAAAGCAAACGGAAATATCTTCGGGAAACACTGTGCAGGACCAG

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 24.70% 12.80% 11.74% 50.72% NA
All Indica  2759 1.40% 9.90% 13.27% 75.35% NA
All Japonica  1512 72.40% 1.70% 10.52% 15.41% NA
Aus  269 0.70% 85.10% 0.74% 13.38% NA
Indica I  595 3.20% 1.30% 4.54% 90.92% NA
Indica II  465 1.10% 20.00% 9.03% 69.89% NA
Indica III  913 0.30% 4.60% 24.64% 70.43% NA
Indica Intermediate  786 1.70% 16.70% 9.16% 72.52% NA
Temperate Japonica  767 94.90% 1.80% 1.04% 2.22% NA
Tropical Japonica  504 31.90% 0.40% 27.58% 40.08% NA
Japonica Intermediate  241 85.10% 4.10% 4.98% 5.81% NA
VI/Aromatic  96 12.50% 67.70% 17.71% 2.08% NA
Intermediate  90 23.30% 12.20% 12.22% 52.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1019539225 T -> G LOC_Os10g36510.1 upstream_gene_variant ; 3105.0bp to feature; MODIFIER silent_mutation Average:62.694; most accessible tissue: Zhenshan97 young leaf, score: 84.814 N N N N
vg1019539225 T -> G LOC_Os10g36530.1 upstream_gene_variant ; 2082.0bp to feature; MODIFIER silent_mutation Average:62.694; most accessible tissue: Zhenshan97 young leaf, score: 84.814 N N N N
vg1019539225 T -> G LOC_Os10g36530.2 upstream_gene_variant ; 2082.0bp to feature; MODIFIER silent_mutation Average:62.694; most accessible tissue: Zhenshan97 young leaf, score: 84.814 N N N N
vg1019539225 T -> G LOC_Os10g36520.1 downstream_gene_variant ; 411.0bp to feature; MODIFIER silent_mutation Average:62.694; most accessible tissue: Zhenshan97 young leaf, score: 84.814 N N N N
vg1019539225 T -> G LOC_Os10g36510-LOC_Os10g36520 intergenic_region ; MODIFIER silent_mutation Average:62.694; most accessible tissue: Zhenshan97 young leaf, score: 84.814 N N N N
vg1019539225 T -> DEL N N silent_mutation Average:62.694; most accessible tissue: Zhenshan97 young leaf, score: 84.814 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)
vg1019539225 T G -0.06 -0.06 -0.04 -0.02 -0.03 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1019539225 NA 2.63E-06 mr1004 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
vg1019539225 NA 4.39E-07 mr1028 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
vg1019539225 NA 8.12E-14 mr1231 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
vg1019539225 NA 3.81E-11 mr1232 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
vg1019539225 NA 2.90E-06 mr1331 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
vg1019539225 NA 3.38E-07 mr1369 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
vg1019539225 NA 1.46E-06 mr1373 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
vg1019539225 NA 1.57E-07 mr1445 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
vg1019539225 NA 3.54E-07 mr1453 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
vg1019539225 NA 2.86E-06 mr1516 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
vg1019539225 NA 1.76E-06 mr1568 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
vg1019539225 NA 2.16E-07 mr1574 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
vg1019539225 NA 9.86E-08 mr1652 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
vg1019539225 2.72E-06 4.90E-09 mr1659 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
vg1019539225 6.06E-06 5.18E-07 mr1659 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
vg1019539225 NA 5.88E-08 mr1735 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
vg1019539225 NA 1.34E-06 mr1762 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
vg1019539225 NA 3.09E-06 mr1659_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