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Detailed information for vg1200826014:

Variant ID: vg1200826014 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 826014
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, A: 0.01, others allele: 0.00, population size: 103. )

Flanking Sequence (100 bp) in Reference Genome:


AATAAGTTGGACTTAGACTAATTTGCAAGTTGCAACCACTAGCTCTCTCTCTCTCTCTCTAGCTAGATTAATTAATATACATATATAGGAGAAGAAGAAC[C/A]
TTCATGCATCTTGCAGTGTGACGCATAAAAACTAAATTAAACTCCTACCACACGCATGCTGAATGGAGCTCATATATATGGACTCAGGTGGTGTTTAGAT

Reverse complement sequence

ATCTAAACACCACCTGAGTCCATATATATGAGCTCCATTCAGCATGCGTGTGGTAGGAGTTTAATTTAGTTTTTATGCGTCACACTGCAAGATGCATGAA[G/T]
GTTCTTCTTCTCCTATATATGTATATTAATTAATCTAGCTAGAGAGAGAGAGAGAGAGCTAGTGGTTGCAACTTGCAAATTAGTCTAAGTCCAACTTATT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 57.20% 42.60% 0.19% 0.00% NA
All Indica  2759 30.20% 69.50% 0.33% 0.00% NA
All Japonica  1512 95.70% 4.30% 0.00% 0.00% NA
Aus  269 98.10% 1.90% 0.00% 0.00% NA
Indica I  595 35.50% 63.70% 0.84% 0.00% NA
Indica II  465 9.20% 90.80% 0.00% 0.00% NA
Indica III  913 39.10% 60.80% 0.11% 0.00% NA
Indica Intermediate  786 28.20% 71.40% 0.38% 0.00% NA
Temperate Japonica  767 94.00% 6.00% 0.00% 0.00% NA
Tropical Japonica  504 96.80% 3.20% 0.00% 0.00% NA
Japonica Intermediate  241 98.80% 1.20% 0.00% 0.00% NA
VI/Aromatic  96 97.90% 2.10% 0.00% 0.00% NA
Intermediate  90 74.40% 25.60% 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
vg1200826014 C -> A LOC_Os12g02440.4 upstream_gene_variant ; 3012.0bp to feature; MODIFIER silent_mutation Average:51.474; most accessible tissue: Zhenshan97 root, score: 96.956 N N N N
vg1200826014 C -> A LOC_Os12g02450.1 upstream_gene_variant ; 221.0bp to feature; MODIFIER silent_mutation Average:51.474; most accessible tissue: Zhenshan97 root, score: 96.956 N N N N
vg1200826014 C -> A LOC_Os12g02440.2 upstream_gene_variant ; 3012.0bp to feature; MODIFIER silent_mutation Average:51.474; most accessible tissue: Zhenshan97 root, score: 96.956 N N N N
vg1200826014 C -> A LOC_Os12g02440.1 upstream_gene_variant ; 3011.0bp to feature; MODIFIER silent_mutation Average:51.474; most accessible tissue: Zhenshan97 root, score: 96.956 N N N N
vg1200826014 C -> A LOC_Os12g02460.1 downstream_gene_variant ; 3501.0bp to feature; MODIFIER silent_mutation Average:51.474; most accessible tissue: Zhenshan97 root, score: 96.956 N N N N
vg1200826014 C -> A LOC_Os12g02450-LOC_Os12g02460 intergenic_region ; MODIFIER silent_mutation Average:51.474; most accessible tissue: Zhenshan97 root, score: 96.956 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)
vg1200826014 C A -0.19 0.05 0.01 0.02 0.0 0.04

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1200826014 NA 3.44E-06 mr1029 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
vg1200826014 NA 2.29E-09 mr1047 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
vg1200826014 NA 3.82E-10 mr1151 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
vg1200826014 NA 7.55E-15 mr1164 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
vg1200826014 NA 4.51E-08 mr1174 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
vg1200826014 NA 1.19E-06 mr1189 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
vg1200826014 NA 7.67E-07 mr1220 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
vg1200826014 NA 7.62E-10 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
vg1200826014 NA 2.59E-15 mr1261 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
vg1200826014 NA 4.43E-06 mr1330 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
vg1200826014 NA 4.23E-06 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
vg1200826014 NA 6.17E-13 mr1503 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
vg1200826014 1.81E-06 1.81E-06 mr1540 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
vg1200826014 2.25E-06 1.95E-06 mr1626 Ind_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
vg1200826014 7.19E-06 NA mr1637 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
vg1200826014 NA 2.21E-06 mr1732 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
vg1200826014 NA 8.70E-06 mr1734 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
vg1200826014 NA 3.23E-06 mr1785 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
vg1200826014 NA 2.66E-07 mr1796 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
vg1200826014 NA 3.87E-15 mr1870 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
vg1200826014 NA 1.24E-07 mr1990 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