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Detailed information for vg1128801387:

Variant ID: vg1128801387 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 28801387
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.68, A: 0.32, others allele: 0.00, population size: 63. )

Flanking Sequence (100 bp) in Reference Genome:


AGGAGGAAGAAAGACTCGAGGTGGTTGGCTGTCGTGTTGTGCATGGCTGCATTCAGAGCCCCGACGGTGATGTCATCGACAGCGTGCCGCTGCACCTGCA[A/G]
CCGGCGTTCGACCACCCGAAGCTCATTCATTTTTGTTTCAATTTGCAGTGATCGTTTCTATCTCCAGCGACGTTTCTTGATCGTGTTTGTGATTGTGTGC

Reverse complement sequence

GCACACAATCACAAACACGATCAAGAAACGTCGCTGGAGATAGAAACGATCACTGCAAATTGAAACAAAAATGAATGAGCTTCGGGTGGTCGAACGCCGG[T/C]
TGCAGGTGCAGCGGCACGCTGTCGATGACATCACCGTCGGGGCTCTGAATGCAGCCATGCACAACACGACAGCCAACCACCTCGAGTCTTTCTTCCTCCT

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 57.10% 40.90% 0.44% 1.54% NA
All Indica  2759 76.00% 21.70% 0.43% 1.85% NA
All Japonica  1512 28.20% 70.70% 0.40% 0.73% NA
Aus  269 32.00% 63.20% 1.12% 3.72% NA
Indica I  595 94.30% 3.70% 0.17% 1.85% NA
Indica II  465 87.70% 11.40% 0.65% 0.22% NA
Indica III  913 60.20% 36.30% 0.44% 3.07% NA
Indica Intermediate  786 73.70% 24.40% 0.51% 1.40% NA
Temperate Japonica  767 46.90% 52.40% 0.65% 0.00% NA
Tropical Japonica  504 7.70% 91.70% 0.20% 0.40% NA
Japonica Intermediate  241 11.20% 85.10% 0.00% 3.73% NA
VI/Aromatic  96 29.20% 69.80% 0.00% 1.04% NA
Intermediate  90 65.60% 34.40% 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
vg1128801387 A -> DEL N N silent_mutation Average:68.995; most accessible tissue: Zhenshan97 panicle, score: 91.992 N N N N
vg1128801387 A -> G LOC_Os11g47760.1 upstream_gene_variant ; 2861.0bp to feature; MODIFIER silent_mutation Average:68.995; most accessible tissue: Zhenshan97 panicle, score: 91.992 N N N N
vg1128801387 A -> G LOC_Os11g47760.2 upstream_gene_variant ; 2861.0bp to feature; MODIFIER silent_mutation Average:68.995; most accessible tissue: Zhenshan97 panicle, score: 91.992 N N N N
vg1128801387 A -> G LOC_Os11g47760.3 upstream_gene_variant ; 2861.0bp to feature; MODIFIER silent_mutation Average:68.995; most accessible tissue: Zhenshan97 panicle, score: 91.992 N N N N
vg1128801387 A -> G LOC_Os11g47760.5 upstream_gene_variant ; 2861.0bp to feature; MODIFIER silent_mutation Average:68.995; most accessible tissue: Zhenshan97 panicle, score: 91.992 N N N N
vg1128801387 A -> G LOC_Os11g47760.6 upstream_gene_variant ; 2861.0bp to feature; MODIFIER silent_mutation Average:68.995; most accessible tissue: Zhenshan97 panicle, score: 91.992 N N N N
vg1128801387 A -> G LOC_Os11g47750.1 downstream_gene_variant ; 1014.0bp to feature; MODIFIER silent_mutation Average:68.995; most accessible tissue: Zhenshan97 panicle, score: 91.992 N N N N
vg1128801387 A -> G LOC_Os11g47740.1 intron_variant ; MODIFIER silent_mutation Average:68.995; most accessible tissue: Zhenshan97 panicle, score: 91.992 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)
vg1128801387 A G 0.02 0.01 0.01 0.02 0.02 0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1128801387 NA 1.98E-09 mr1260 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
vg1128801387 NA 1.60E-09 mr1300 Jap_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
vg1128801387 2.81E-06 2.52E-11 mr1310 Jap_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
vg1128801387 NA 9.98E-07 mr1336 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
vg1128801387 NA 1.08E-10 mr1926 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
vg1128801387 NA 2.96E-06 mr1959 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
vg1128801387 NA 1.90E-11 mr1310_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
vg1128801387 NA 5.96E-08 mr1959_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