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Detailed information for vg1101821019:

Variant ID: vg1101821019 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 1821019
Reference Allele: TAlternative Allele: G
Primary Allele: TSecondary Allele: G

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.58, G: 0.42, others allele: 0.00, population size: 107. )

Flanking Sequence (100 bp) in Reference Genome:


GTTATGGAATCAGTTTTATCAATAATCTACGTTTAATAATCTAAAATAACAAGATTTCGGAGGGCTATTTAATAGCCCGGAGGATCCAGGCTTTTCTTCA[T/G]
GTTCACTCAAAGTTAACACAGGAAATAATCCAATATATGAAGTCCTGTCCAATCACATTGCATCGCCATCACTTGAGTCCGTTTATCCAAGTATCCAACC

Reverse complement sequence

GGTTGGATACTTGGATAAACGGACTCAAGTGATGGCGATGCAATGTGATTGGACAGGACTTCATATATTGGATTATTTCCTGTGTTAACTTTGAGTGAAC[A/C]
TGAAGAAAAGCCTGGATCCTCCGGGCTATTAAATAGCCCTCCGAAATCTTGTTATTTTAGATTATTAAACGTAGATTATTGATAAAACTGATTCCATAAC

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 54.90% 45.00% 0.08% 0.00% NA
All Indica  2759 31.60% 68.30% 0.07% 0.00% NA
All Japonica  1512 97.60% 2.30% 0.07% 0.00% NA
Aus  269 53.50% 46.10% 0.37% 0.00% NA
Indica I  595 91.90% 8.10% 0.00% 0.00% NA
Indica II  465 12.70% 87.30% 0.00% 0.00% NA
Indica III  913 3.10% 96.80% 0.11% 0.00% NA
Indica Intermediate  786 30.40% 69.50% 0.13% 0.00% NA
Temperate Japonica  767 98.00% 2.00% 0.00% 0.00% NA
Tropical Japonica  504 97.00% 3.00% 0.00% 0.00% NA
Japonica Intermediate  241 97.50% 2.10% 0.41% 0.00% NA
VI/Aromatic  96 43.80% 56.20% 0.00% 0.00% NA
Intermediate  90 66.70% 33.30% 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
vg1101821019 T -> G LOC_Os11g04370.1 upstream_gene_variant ; 4258.0bp to feature; MODIFIER silent_mutation Average:92.39; most accessible tissue: Callus, score: 95.765 N N N N
vg1101821019 T -> G LOC_Os11g04390.1 upstream_gene_variant ; 340.0bp to feature; MODIFIER silent_mutation Average:92.39; most accessible tissue: Callus, score: 95.765 N N N N
vg1101821019 T -> G LOC_Os11g04390.2 upstream_gene_variant ; 354.0bp to feature; MODIFIER silent_mutation Average:92.39; most accessible tissue: Callus, score: 95.765 N N N N
vg1101821019 T -> G LOC_Os11g04390.3 upstream_gene_variant ; 354.0bp to feature; MODIFIER silent_mutation Average:92.39; most accessible tissue: Callus, score: 95.765 N N N N
vg1101821019 T -> G LOC_Os11g04380.1 downstream_gene_variant ; 515.0bp to feature; MODIFIER silent_mutation Average:92.39; most accessible tissue: Callus, score: 95.765 N N N N
vg1101821019 T -> G LOC_Os11g04380-LOC_Os11g04390 intergenic_region ; MODIFIER silent_mutation Average:92.39; most accessible tissue: Callus, score: 95.765 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)
vg1101821019 T G 0.0 0.0 0.0 0.01 0.0 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1101821019 NA 2.80E-15 mr1565 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
vg1101821019 NA 1.77E-10 mr1904 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
vg1101821019 NA 3.62E-07 mr1024_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
vg1101821019 NA 2.78E-07 mr1184_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
vg1101821019 NA 8.74E-06 mr1199_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
vg1101821019 NA 2.35E-06 mr1278_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
vg1101821019 NA 6.23E-07 mr1418_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
vg1101821019 NA 5.83E-06 mr1419_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
vg1101821019 NA 1.45E-06 mr1420_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
vg1101821019 NA 1.65E-07 mr1488_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
vg1101821019 NA 1.11E-06 mr1556_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
vg1101821019 NA 6.55E-07 mr1558_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
vg1101821019 NA 1.93E-17 mr1565_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
vg1101821019 NA 6.18E-12 mr1565_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
vg1101821019 NA 6.25E-09 mr1598_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
vg1101821019 NA 6.82E-12 mr1636_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
vg1101821019 NA 1.58E-12 mr1641_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
vg1101821019 NA 9.51E-06 mr1641_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
vg1101821019 NA 2.11E-11 mr1659_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
vg1101821019 NA 3.29E-07 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
vg1101821019 NA 3.24E-09 mr1683_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
vg1101821019 NA 8.22E-06 mr1706_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
vg1101821019 NA 2.67E-16 mr1715_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
vg1101821019 NA 6.72E-06 mr1764_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
vg1101821019 NA 4.29E-15 mr1767_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
vg1101821019 NA 3.94E-06 mr1779_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
vg1101821019 NA 4.71E-06 mr1835_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
vg1101821019 NA 1.91E-16 mr1838_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
vg1101821019 NA 2.40E-06 mr1838_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
vg1101821019 NA 8.93E-09 mr1861_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
vg1101821019 NA 4.25E-07 mr1904_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
vg1101821019 NA 1.48E-07 mr1921_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