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Detailed information for vg1210770515:

Variant ID: vg1210770515 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 10770515
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.60, A: 0.40, others allele: 0.00, population size: 68. )

Flanking Sequence (100 bp) in Reference Genome:


TTTTGTTTTACCTGTGCTACGGTCAAAATGTTTAGAAAGGTCGGAGGGAGTACTATGCTTGTGTTTAGTGCCACGTTAAAATTGGAAGTTTGAAGAAATT[A/G]
AAACAATGTGACAGAAAAGTTAGAAGTTTGTGTGTAGTAAAATTCGATGTTATGGAAAAGTTAAAAATTTAAAGAAAAAAGTTGAAATCTAACCAGGACC

Reverse complement sequence

GGTCCTGGTTAGATTTCAACTTTTTTCTTTAAATTTTTAACTTTTCCATAACATCGAATTTTACTACACACAAACTTCTAACTTTTCTGTCACATTGTTT[T/C]
AATTTCTTCAAACTTCCAATTTTAACGTGGCACTAAACACAAGCATAGTACTCCCTCCGACCTTTCTAAACATTTTGACCGTAGCACAGGTAAAACAAAA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 50.30% 49.60% 0.19% 0.00% NA
All Indica  2759 57.60% 42.20% 0.25% 0.00% NA
All Japonica  1512 30.20% 69.70% 0.07% 0.00% NA
Aus  269 81.00% 18.60% 0.37% 0.00% NA
Indica I  595 60.70% 39.30% 0.00% 0.00% NA
Indica II  465 51.80% 48.00% 0.22% 0.00% NA
Indica III  913 54.40% 45.30% 0.22% 0.00% NA
Indica Intermediate  786 62.30% 37.20% 0.51% 0.00% NA
Temperate Japonica  767 21.80% 78.20% 0.00% 0.00% NA
Tropical Japonica  504 35.70% 64.30% 0.00% 0.00% NA
Japonica Intermediate  241 45.60% 53.90% 0.41% 0.00% NA
VI/Aromatic  96 74.00% 26.00% 0.00% 0.00% NA
Intermediate  90 44.40% 55.60% 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
vg1210770515 A -> G LOC_Os12g18650.1 upstream_gene_variant ; 440.0bp to feature; MODIFIER silent_mutation Average:90.957; most accessible tissue: Callus, score: 95.811 N N N N
vg1210770515 A -> G LOC_Os12g18650.7 upstream_gene_variant ; 440.0bp to feature; MODIFIER silent_mutation Average:90.957; most accessible tissue: Callus, score: 95.811 N N N N
vg1210770515 A -> G LOC_Os12g18650.2 upstream_gene_variant ; 450.0bp to feature; MODIFIER silent_mutation Average:90.957; most accessible tissue: Callus, score: 95.811 N N N N
vg1210770515 A -> G LOC_Os12g18650.6 upstream_gene_variant ; 450.0bp to feature; MODIFIER silent_mutation Average:90.957; most accessible tissue: Callus, score: 95.811 N N N N
vg1210770515 A -> G LOC_Os12g18650.3 upstream_gene_variant ; 463.0bp to feature; MODIFIER silent_mutation Average:90.957; most accessible tissue: Callus, score: 95.811 N N N N
vg1210770515 A -> G LOC_Os12g18650.5 upstream_gene_variant ; 463.0bp to feature; MODIFIER silent_mutation Average:90.957; most accessible tissue: Callus, score: 95.811 N N N N
vg1210770515 A -> G LOC_Os12g18650.4 upstream_gene_variant ; 1347.0bp to feature; MODIFIER silent_mutation Average:90.957; most accessible tissue: Callus, score: 95.811 N N N N
vg1210770515 A -> G LOC_Os12g18640.1 downstream_gene_variant ; 1479.0bp to feature; MODIFIER silent_mutation Average:90.957; most accessible tissue: Callus, score: 95.811 N N N N
vg1210770515 A -> G LOC_Os12g18640-LOC_Os12g18650 intergenic_region ; MODIFIER silent_mutation Average:90.957; most accessible tissue: Callus, score: 95.811 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)
vg1210770515 A G -0.02 -0.03 -0.03 -0.02 -0.02 -0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1210770515 NA 5.38E-08 mr1156 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
vg1210770515 NA 1.81E-08 mr1164 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
vg1210770515 NA 6.58E-06 mr1179 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
vg1210770515 NA 4.14E-07 mr1280 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
vg1210770515 NA 9.62E-07 mr1293 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
vg1210770515 NA 1.54E-06 mr1294 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
vg1210770515 NA 4.78E-06 mr1315 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
vg1210770515 NA 3.30E-06 mr1318 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
vg1210770515 NA 4.76E-06 mr1392 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
vg1210770515 3.57E-06 3.57E-06 mr1418 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
vg1210770515 NA 9.12E-06 mr1419 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
vg1210770515 NA 8.67E-07 mr1494 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
vg1210770515 NA 1.26E-07 mr1507 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
vg1210770515 NA 1.48E-06 mr1604 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
vg1210770515 NA 8.41E-08 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
vg1210770515 NA 4.39E-07 mr1809 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
vg1210770515 NA 7.64E-07 mr1810 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
vg1210770515 3.98E-06 3.98E-06 mr1813 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
vg1210770515 NA 7.82E-06 mr1937 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
vg1210770515 NA 1.07E-08 mr1164_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
vg1210770515 NA 4.22E-06 mr1425_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