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Detailed information for vg0204032926:

Variant ID: vg0204032926 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 4032926
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, T: 0.00, others allele: 0.00, population size: 295. )

Flanking Sequence (100 bp) in Reference Genome:


CCTACTCGGTGTTCCCTGATGCTCAACAATTCCTGAGATGGCTGCGCAACAATGGCTGCACCGTCGGTATCGTCAGCAACGCCGAGTACCGGTACAAGGA[C/T]
GTCGTCCTACCTGCACTTGGTCTCAATGAGGTAAATTCTGCAAATTTTTCTGCAGATATTATCAGCTGATTAATCGAACCACAAAATTCACAATTACTCC

Reverse complement sequence

GGAGTAATTGTGAATTTTGTGGTTCGATTAATCAGCTGATAATATCTGCAGAAAAATTTGCAGAATTTACCTCATTGAGACCAAGTGCAGGTAGGACGAC[G/A]
TCCTTGTACCGGTACTCGGCGTTGCTGACGATACCGACGGTGCAGCCATTGTTGCGCAGCCATCTCAGGAATTGTTGAGCATCAGGGAACACCGAGTAGG

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 67.30% 32.30% 0.42% 0.00% NA
All Indica  2759 66.90% 33.00% 0.07% 0.00% NA
All Japonica  1512 66.10% 32.90% 1.06% 0.00% NA
Aus  269 98.90% 0.40% 0.74% 0.00% NA
Indica I  595 61.70% 38.30% 0.00% 0.00% NA
Indica II  465 74.20% 25.60% 0.22% 0.00% NA
Indica III  913 60.90% 39.10% 0.00% 0.00% NA
Indica Intermediate  786 73.50% 26.30% 0.13% 0.00% NA
Temperate Japonica  767 93.70% 4.60% 1.69% 0.00% NA
Tropical Japonica  504 30.40% 69.20% 0.40% 0.00% NA
Japonica Intermediate  241 52.70% 46.90% 0.41% 0.00% NA
VI/Aromatic  96 7.30% 92.70% 0.00% 0.00% NA
Intermediate  90 67.80% 32.20% 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
vg0204032926 C -> T LOC_Os02g07730.1 synonymous_variant ; p.Asp145Asp; LOW synonymous_codon Average:76.229; most accessible tissue: Zhenshan97 flag leaf, score: 89.624 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)
vg0204032926 C T -0.01 -0.01 -0.01 -0.01 -0.01 -0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0204032926 NA 1.55E-09 mr1229 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
vg0204032926 NA 5.81E-09 mr1739 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
vg0204032926 NA 3.92E-06 mr1363_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
vg0204032926 NA 5.15E-09 mr1980_2 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