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Detailed information for vg0920815305:

Variant ID: vg0920815305 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 20815305
Reference Allele: TAlternative Allele: A
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.95, T: 0.06, others allele: 0.00, population size: 113. )

Flanking Sequence (100 bp) in Reference Genome:


ACACCCAAAACTTTTATTTTCGTGAACTAAACACGTCCGTAGCTGATGAAAAACGGATACTCCATAATGTCAATGTCAAAAAAAAAAAAACGGATACTCC[T/A]
GGACTGGGAAAACATTGCCAAAAGAGGAGCGAATGCCAGCACCTGAACTGGAGTACTTCGAGTCATCCTCTCTAGCTACAGAAATGTAGTAAATGAAGTT

Reverse complement sequence

AACTTCATTTACTACATTTCTGTAGCTAGAGAGGATGACTCGAAGTACTCCAGTTCAGGTGCTGGCATTCGCTCCTCTTTTGGCAATGTTTTCCCAGTCC[A/T]
GGAGTATCCGTTTTTTTTTTTTTGACATTGACATTATGGAGTATCCGTTTTTCATCAGCTACGGACGTGTTTAGTTCACGAAAATAAAAGTTTTGGGTGT

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 59.80% 40.00% 0.17% 0.02% NA
All Indica  2759 91.00% 8.70% 0.25% 0.04% NA
All Japonica  1512 0.60% 99.40% 0.00% 0.00% NA
Aus  269 99.30% 0.70% 0.00% 0.00% NA
Indica I  595 91.40% 7.90% 0.67% 0.00% NA
Indica II  465 93.30% 6.50% 0.00% 0.22% NA
Indica III  913 91.10% 8.80% 0.11% 0.00% NA
Indica Intermediate  786 89.10% 10.70% 0.25% 0.00% NA
Temperate Japonica  767 0.10% 99.90% 0.00% 0.00% NA
Tropical Japonica  504 0.00% 100.00% 0.00% 0.00% NA
Japonica Intermediate  241 3.30% 96.70% 0.00% 0.00% NA
VI/Aromatic  96 12.50% 87.50% 0.00% 0.00% NA
Intermediate  90 33.30% 65.60% 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
vg0920815305 T -> DEL N N silent_mutation Average:46.267; most accessible tissue: Zhenshan97 flower, score: 81.325 N N N N
vg0920815305 T -> A LOC_Os09g36140.1 upstream_gene_variant ; 2135.0bp to feature; MODIFIER silent_mutation Average:46.267; most accessible tissue: Zhenshan97 flower, score: 81.325 N N N N
vg0920815305 T -> A LOC_Os09g36140-LOC_Os09g36150 intergenic_region ; MODIFIER silent_mutation Average:46.267; most accessible tissue: Zhenshan97 flower, score: 81.325 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)
vg0920815305 T A -0.04 -0.04 -0.03 -0.03 -0.08 -0.08

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0920815305 NA 3.07E-08 mr1201 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
vg0920815305 NA 1.89E-10 mr1219 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
vg0920815305 NA 3.09E-08 mr1274 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
vg0920815305 NA 1.73E-29 mr1333 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
vg0920815305 5.28E-06 2.57E-22 mr1518 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
vg0920815305 7.07E-06 6.65E-07 mr1518 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
vg0920815305 NA 4.04E-36 mr1542 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
vg0920815305 NA 4.42E-24 mr1676 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
vg0920815305 9.35E-06 2.60E-08 mr1676 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
vg0920815305 NA 7.00E-20 mr1754 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
vg0920815305 NA 1.81E-07 mr1201_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
vg0920815305 1.41E-06 1.08E-10 mr1219_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
vg0920815305 2.17E-07 1.54E-10 mr1274_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
vg0920815305 NA 1.25E-18 mr1657_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
vg0920815305 NA 5.62E-26 mr1676_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
vg0920815305 NA 2.03E-08 mr1676_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