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Detailed information for vg1121207085:

Variant ID: vg1121207085 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 21207085
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.71, G: 0.29, others allele: 0.00, population size: 200. )

Flanking Sequence (100 bp) in Reference Genome:


AGATTTTCGAAGTTTCAGTCATCCTTCAGAGATTCTTCTGAGCAACAGCAACAGTTTGAGTATGGTCCCAGACCAAGTTGTTGAATTTCTTATGTCGGCA[G/A]
ATCAGTTTGTCTGCTATTTGTTGAATTTGATGTCGGCAGGTCAGCTTGTCTGCTATAGAGTTCAGTTTTGTTTGGTATGGATTTAGCGTCTTGTAGATGC

Reverse complement sequence

GCATCTACAAGACGCTAAATCCATACCAAACAAAACTGAACTCTATAGCAGACAAGCTGACCTGCCGACATCAAATTCAACAAATAGCAGACAAACTGAT[C/T]
TGCCGACATAAGAAATTCAACAACTTGGTCTGGGACCATACTCAAACTGTTGCTGTTGCTCAGAAGAATCTCTGAAGGATGACTGAAACTTCGAAAATCT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 54.20% 45.60% 0.15% 0.00% NA
All Indica  2759 58.40% 41.50% 0.18% 0.00% NA
All Japonica  1512 50.70% 49.20% 0.07% 0.00% NA
Aus  269 17.50% 82.50% 0.00% 0.00% NA
Indica I  595 32.40% 67.60% 0.00% 0.00% NA
Indica II  465 68.60% 31.40% 0.00% 0.00% NA
Indica III  913 66.90% 33.00% 0.11% 0.00% NA
Indica Intermediate  786 62.00% 37.50% 0.51% 0.00% NA
Temperate Japonica  767 19.00% 80.80% 0.13% 0.00% NA
Tropical Japonica  504 86.30% 13.70% 0.00% 0.00% NA
Japonica Intermediate  241 77.20% 22.80% 0.00% 0.00% NA
VI/Aromatic  96 93.80% 6.20% 0.00% 0.00% NA
Intermediate  90 54.40% 44.40% 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
vg1121207085 G -> A LOC_Os11g36070.1 3_prime_UTR_variant ; 514.0bp to feature; MODIFIER silent_mutation Average:75.313; most accessible tissue: Minghui63 young leaf, score: 89.224 N N N N
vg1121207085 G -> A LOC_Os11g36070.4 3_prime_UTR_variant ; 514.0bp to feature; MODIFIER silent_mutation Average:75.313; most accessible tissue: Minghui63 young leaf, score: 89.224 N N N N
vg1121207085 G -> A LOC_Os11g36070.3 3_prime_UTR_variant ; 514.0bp to feature; MODIFIER silent_mutation Average:75.313; most accessible tissue: Minghui63 young leaf, score: 89.224 N N N N
vg1121207085 G -> A LOC_Os11g36070.2 3_prime_UTR_variant ; 514.0bp to feature; MODIFIER silent_mutation Average:75.313; most accessible tissue: Minghui63 young leaf, score: 89.224 N N N N
vg1121207085 G -> A LOC_Os11g36090.1 downstream_gene_variant ; 3626.0bp to feature; MODIFIER silent_mutation Average:75.313; most accessible tissue: Minghui63 young leaf, score: 89.224 N N N N
vg1121207085 G -> A LOC_Os11g36070.5 downstream_gene_variant ; 3458.0bp to feature; MODIFIER silent_mutation Average:75.313; most accessible tissue: Minghui63 young leaf, score: 89.224 N N N N
vg1121207085 G -> A LOC_Os11g36070.6 downstream_gene_variant ; 3097.0bp to feature; MODIFIER silent_mutation Average:75.313; most accessible tissue: Minghui63 young leaf, score: 89.224 N N N N
vg1121207085 G -> A LOC_Os11g36070.7 downstream_gene_variant ; 2989.0bp to feature; MODIFIER silent_mutation Average:75.313; most accessible tissue: Minghui63 young leaf, score: 89.224 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)
vg1121207085 G A -0.02 -0.02 -0.02 -0.01 -0.01 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1121207085 NA 2.44E-06 mr1013 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
vg1121207085 NA 4.48E-07 mr1030 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
vg1121207085 NA 1.63E-06 mr1034 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
vg1121207085 NA 1.65E-06 mr1042 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
vg1121207085 NA 8.21E-07 mr1324 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
vg1121207085 NA 7.48E-07 mr1397 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
vg1121207085 NA 1.50E-06 mr1479 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
vg1121207085 NA 6.11E-09 mr1502 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
vg1121207085 NA 3.12E-06 mr1502 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
vg1121207085 NA 8.36E-06 mr1502 Jap_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
vg1121207085 NA 5.32E-06 mr1543 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
vg1121207085 NA 2.19E-06 mr1596 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
vg1121207085 NA 3.83E-07 mr1729 Jap_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
vg1121207085 NA 2.54E-07 mr1742 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
vg1121207085 NA 1.11E-06 mr1880 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
vg1121207085 NA 4.29E-06 mr1892 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
vg1121207085 NA 3.02E-06 mr1912 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
vg1121207085 NA 5.62E-07 mr1965 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
vg1121207085 NA 6.28E-06 mr1975 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
vg1121207085 NA 1.81E-06 mr1986 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
vg1121207085 NA 2.48E-07 mr1042_2 Jap_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
vg1121207085 NA 1.08E-07 mr1274_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
vg1121207085 NA 3.72E-07 mr1274_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
vg1121207085 NA 4.62E-09 mr1742_2 Jap_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
vg1121207085 NA 3.57E-08 mr1871_2 Jap_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