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Detailed information for vg0723280519:

Variant ID: vg0723280519 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 23280519
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, T: 0.03, others allele: 0.00, population size: 107. )

Flanking Sequence (100 bp) in Reference Genome:


GGTTGCTGCTGATGTCGTGGAACTCGGGGTTCATGATGGTGTCCAGCTCGACGGCCAGGATTTGGCCGCTCGCCGTGCCGTTCGTCGCGTTGAGGAAGCC[C/T]
AGGTACTGCCCGGCGTTCGCCGCCGAGAGGTTCGCCGTCGGCGCGACCACGAACGCGAGCCCGTGGTCGCTCAGGCCGTCGTACCCGGACACGATGGCGA

Reverse complement sequence

TCGCCATCGTGTCCGGGTACGACGGCCTGAGCGACCACGGGCTCGCGTTCGTGGTCGCGCCGACGGCGAACCTCTCGGCGGCGAACGCCGGGCAGTACCT[G/A]
GGCTTCCTCAACGCGACGAACGGCACGGCGAGCGGCCAAATCCTGGCCGTCGAGCTGGACACCATCATGAACCCCGAGTTCCACGACATCAGCAGCAACC

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 56.50% 43.20% 0.25% 0.02% NA
All Indica  2759 29.70% 69.90% 0.33% 0.04% NA
All Japonica  1512 99.70% 0.10% 0.20% 0.00% NA
Aus  269 66.20% 33.80% 0.00% 0.00% NA
Indica I  595 6.90% 93.10% 0.00% 0.00% NA
Indica II  465 37.20% 61.70% 1.08% 0.00% NA
Indica III  913 35.50% 64.30% 0.22% 0.00% NA
Indica Intermediate  786 35.90% 63.70% 0.25% 0.13% NA
Temperate Japonica  767 99.70% 0.10% 0.13% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 98.80% 0.40% 0.83% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 76.70% 23.30% 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
vg0723280519 C -> DEL LOC_Os07g38800.1 N frameshift_variant Average:81.388; most accessible tissue: Zhenshan97 flag leaf, score: 92.971 N N N N
vg0723280519 C -> T LOC_Os07g38800.1 synonymous_variant ; p.Leu145Leu; LOW synonymous_codon Average:81.388; most accessible tissue: Zhenshan97 flag leaf, score: 92.971 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)
vg0723280519 C T -0.05 -0.03 -0.04 0.0 -0.03 -0.06

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0723280519 NA 1.26E-09 mr1352 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
vg0723280519 4.07E-06 NA mr1743 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
vg0723280519 NA 3.40E-06 mr1743 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
vg0723280519 NA 3.15E-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
vg0723280519 NA 4.73E-06 mr1074_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