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Detailed information for vg0921059996:

Variant ID: vg0921059996 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 21059996
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.02, others allele: 0.00, population size: 100. )

Flanking Sequence (100 bp) in Reference Genome:


GGCTGGGATGGCAGCACAAACACCACCACCAGCCTCCGCTCATGGAACCGCGCCGCGCCGCGGTCCTCCTCCTCCTCCACCACCACCGCGTCCACCTCCT[C/T]
AGCCTTGGCGGCGCCGGCGACATCAAGAAGGAGTCGGCGCCGGCGGGGCCTCGGTTGTGCAGCTCCTGTCCTGCCGTCTGCCGCAGCTAGGGCCAACTCC

Reverse complement sequence

GGAGTTGGCCCTAGCTGCGGCAGACGGCAGGACAGGAGCTGCACAACCGAGGCCCCGCCGGCGCCGACTCCTTCTTGATGTCGCCGGCGCCGCCAAGGCT[G/A]
AGGAGGTGGACGCGGTGGTGGTGGAGGAGGAGGAGGACCGCGGCGCGGCGCGGTTCCATGAGCGGAGGCTGGTGGTGGTGTTTGTGCTGCCATCCCAGCC

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 65.10% 34.70% 0.19% 0.00% NA
All Indica  2759 40.60% 59.20% 0.29% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 36.50% 62.70% 0.84% 0.00% NA
Indica II  465 33.80% 66.00% 0.22% 0.00% NA
Indica III  913 40.30% 59.50% 0.22% 0.00% NA
Indica Intermediate  786 48.00% 52.00% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 87.80% 11.10% 1.11% 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
vg0921059996 C -> T LOC_Os09g36510.1 missense_variant ; p.Ser97Leu; MODERATE nonsynonymous_codon ; S97L Average:95.419; most accessible tissue: Zhenshan97 flag leaf, score: 99.094 unknown unknown DELETERIOUS 0.03

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)
vg0921059996 C T -0.02 -0.02 -0.02 -0.03 -0.02 -0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0921059996 NA 3.70E-06 mr1181 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
vg0921059996 NA 5.75E-07 mr1321 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
vg0921059996 3.57E-06 4.80E-08 mr1568 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
vg0921059996 NA 1.73E-09 mr1610 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