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Detailed information for vg0103093065:

Variant ID: vg0103093065 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 3093065
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATCATCTAATCTCATATGATATTTTTAGAGATAATACATTAAGTATTAATGTCCTAGAGCACTTGCTCTCACAAACACGGACTTTCAGATCACGTGAAAA[A/G]
AGCCTTTTTGTTTGGGATTGTTTCGTTCATAAAATACCCTTTTTTGTTTTGGTTGCAGAGAAAATACTGGTGGCCTACAGTGATCCATGTATGCAGCATG

Reverse complement sequence

CATGCTGCATACATGGATCACTGTAGGCCACCAGTATTTTCTCTGCAACCAAAACAAAAAAGGGTATTTTATGAACGAAACAATCCCAAACAAAAAGGCT[T/C]
TTTTCACGTGATCTGAAAGTCCGTGTTTGTGAGAGCAAGTGCTCTAGGACATTAATACTTAATGTATTATCTCTAAAAATATCATATGAGATTAGATGAT

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 88.20% 10.70% 1.10% 0.00% NA
All Indica  2759 98.10% 1.90% 0.00% 0.00% NA
All Japonica  1512 74.30% 22.40% 3.31% 0.00% NA
Aus  269 90.30% 9.70% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 97.40% 2.60% 0.00% 0.00% NA
Indica III  913 96.20% 3.80% 0.00% 0.00% NA
Indica Intermediate  786 99.20% 0.80% 0.00% 0.00% NA
Temperate Japonica  767 59.50% 34.60% 6.00% 0.00% NA
Tropical Japonica  504 98.60% 1.40% 0.00% 0.00% NA
Japonica Intermediate  241 70.50% 27.80% 1.66% 0.00% NA
VI/Aromatic  96 16.70% 81.20% 2.08% 0.00% NA
Intermediate  90 91.10% 8.90% 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
vg0103093065 A -> G LOC_Os01g06550.1 upstream_gene_variant ; 2178.0bp to feature; MODIFIER silent_mutation Average:95.838; most accessible tissue: Callus, score: 99.854 N N N N
vg0103093065 A -> G LOC_Os01g06560.1 upstream_gene_variant ; 200.0bp to feature; MODIFIER silent_mutation Average:95.838; most accessible tissue: Callus, score: 99.854 N N N N
vg0103093065 A -> G LOC_Os01g06570.1 upstream_gene_variant ; 2145.0bp to feature; MODIFIER silent_mutation Average:95.838; most accessible tissue: Callus, score: 99.854 N N N N
vg0103093065 A -> G LOC_Os01g06560.2 upstream_gene_variant ; 200.0bp to feature; MODIFIER silent_mutation Average:95.838; most accessible tissue: Callus, score: 99.854 N N N N
vg0103093065 A -> G LOC_Os01g06580.1 downstream_gene_variant ; 4281.0bp to feature; MODIFIER silent_mutation Average:95.838; most accessible tissue: Callus, score: 99.854 N N N N
vg0103093065 A -> G LOC_Os01g06560-LOC_Os01g06570 intergenic_region ; MODIFIER silent_mutation Average:95.838; most accessible tissue: Callus, score: 99.854 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)
vg0103093065 A G 0.0 0.0 0.0 0.01 0.01 0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0103093065 NA 2.33E-11 Heading_date Jap_All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0103093065 NA 2.32E-06 mr1092 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
vg0103093065 9.67E-07 3.42E-08 mr1354 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
vg0103093065 NA 2.96E-09 mr1354 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
vg0103093065 3.94E-06 3.49E-11 mr1829 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
vg0103093065 NA 4.26E-07 mr1829 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
vg0103093065 NA 1.04E-06 mr1045_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
vg0103093065 NA 2.73E-06 mr1045_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
vg0103093065 3.08E-06 NA mr1354_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
vg0103093065 NA 5.61E-09 mr1354_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
vg0103093065 2.78E-06 1.01E-13 mr1567_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
vg0103093065 NA 3.50E-10 mr1567_2 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
vg0103093065 8.57E-06 8.57E-06 mr1806_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
vg0103093065 3.12E-09 8.43E-18 mr1829_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
vg0103093065 NA 1.16E-10 mr1829_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
vg0103093065 NA 1.18E-16 mr1842_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
vg0103093065 3.06E-08 1.67E-21 mr1902_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
vg0103093065 NA 2.48E-10 mr1902_2 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