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Detailed information for vg1015010798:

Variant ID: vg1015010798 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 15010798
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CCAGGTCCTTGACAAGAGATGGGCAGCTCTGCATCAGATGCAGGAAGCCGTCGGTCGCCATCACCGCGTTCAGCGTCTCCTTCGACTCGAGGAACCGGAA[G/A]
CACGCCTCCTTGAGGGCTTGGCAATGGTGCTGCTCTGCCAACGCCATGAGCGTCGCCACCGAGCCCCGGTCGATGTACTCGACCACCTTCTCCTCGCAGA

Reverse complement sequence

TCTGCGAGGAGAAGGTGGTCGAGTACATCGACCGGGGCTCGGTGGCGACGCTCATGGCGTTGGCAGAGCAGCACCATTGCCAAGCCCTCAAGGAGGCGTG[C/T]
TTCCGGTTCCTCGAGTCGAAGGAGACGCTGAACGCGGTGATGGCGACCGACGGCTTCCTGCATCTGATGCAGAGCTGCCCATCTCTTGTCAAGGACCTGG

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 56.20% 37.20% 4.66% 1.99% NA
All Indica  2759 84.80% 4.00% 7.83% 3.37% NA
All Japonica  1512 0.70% 99.20% 0.13% 0.00% NA
Aus  269 99.30% 0.40% 0.37% 0.00% NA
Indica I  595 87.60% 5.00% 4.87% 2.52% NA
Indica II  465 69.90% 6.50% 15.70% 7.96% NA
Indica III  913 93.30% 1.00% 4.82% 0.88% NA
Indica Intermediate  786 81.70% 5.20% 8.91% 4.20% NA
Temperate Japonica  767 0.10% 99.90% 0.00% 0.00% NA
Tropical Japonica  504 1.00% 98.80% 0.20% 0.00% NA
Japonica Intermediate  241 1.70% 97.90% 0.41% 0.00% NA
VI/Aromatic  96 1.00% 99.00% 0.00% 0.00% NA
Intermediate  90 40.00% 57.80% 1.11% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1015010798 G -> A LOC_Os10g28780.1 synonymous_variant ; p.Cys340Cys; LOW synonymous_codon Average:84.424; most accessible tissue: Zhenshan97 flower, score: 93.007 N N N N
vg1015010798 G -> DEL LOC_Os10g28780.1 N frameshift_variant Average:84.424; most accessible tissue: Zhenshan97 flower, score: 93.007 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)
vg1015010798 G A 0.02 0.01 0.01 0.01 0.03 0.03

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1015010798 NA 1.85E-70 mr1027 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
vg1015010798 NA 1.57E-73 mr1135 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
vg1015010798 NA 8.36E-66 mr1538 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
vg1015010798 NA 3.70E-36 mr1542 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
vg1015010798 NA 3.51E-43 mr1591 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
vg1015010798 NA 1.11E-59 mr1594 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
vg1015010798 NA 2.12E-08 mr1595 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
vg1015010798 NA 4.96E-41 mr1645 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
vg1015010798 NA 1.52E-31 mr1647 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
vg1015010798 NA 3.62E-09 mr1663 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
vg1015010798 NA 1.85E-89 mr1758 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
vg1015010798 3.44E-06 9.79E-07 mr1758 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
vg1015010798 NA 5.48E-39 mr1890 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
vg1015010798 NA 1.19E-42 mr1891 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
vg1015010798 NA 1.36E-98 mr1987 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
vg1015010798 NA 1.99E-18 mr1657_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