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Detailed information for vg0221587239:

Variant ID: vg0221587239 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 21587239
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 232. )

Flanking Sequence (100 bp) in Reference Genome:


CTTCCCCGTCGTCGTACGCAGCAGGGAACCAGTGCTCGGGGATGAGAGGGACATGAGATCCGGCCGGCGCGGCCCACGAGATCAGCGTCCTGTGCGACGC[T/C]
GAGGTCGGCGTCGTCTTCTTCTCCAGCGCCGACAAGCTCTACGACTACTGCTCCCCCAAGACCTTGTGCGTGCCCTCCGTACGTTCTCACTCTTCTCTTC

Reverse complement sequence

GAAGAGAAGAGTGAGAACGTACGGAGGGCACGCACAAGGTCTTGGGGGAGCAGTAGTCGTAGAGCTTGTCGGCGCTGGAGAAGAAGACGACGCCGACCTC[A/G]
GCGTCGCACAGGACGCTGATCTCGTGGGCCGCGCCGGCCGGATCTCATGTCCCTCTCATCCCCGAGCACTGGTTCCCTGCTGCGTACGACGACGGGGAAG

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 65.00% 31.10% 0.70% 3.20% NA
All Indica  2759 97.70% 1.40% 0.14% 0.76% NA
All Japonica  1512 3.70% 89.40% 1.52% 5.36% NA
Aus  269 99.30% 0.70% 0.00% 0.00% NA
Indica I  595 98.50% 1.00% 0.00% 0.50% NA
Indica II  465 98.70% 0.60% 0.22% 0.43% NA
Indica III  913 98.20% 1.00% 0.11% 0.66% NA
Indica Intermediate  786 95.90% 2.50% 0.25% 1.27% NA
Temperate Japonica  767 1.60% 93.10% 1.17% 4.17% NA
Tropical Japonica  504 7.30% 82.10% 2.18% 8.33% NA
Japonica Intermediate  241 2.90% 92.90% 1.24% 2.90% NA
VI/Aromatic  96 12.50% 42.70% 5.21% 39.58% NA
Intermediate  90 43.30% 43.30% 1.11% 12.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0221587239 T -> DEL N N silent_mutation Average:89.241; most accessible tissue: Zhenshan97 young leaf, score: 94.425 N N N N
vg0221587239 T -> C LOC_Os02g35930.1 upstream_gene_variant ; 3697.0bp to feature; MODIFIER silent_mutation Average:89.241; most accessible tissue: Zhenshan97 young leaf, score: 94.425 N N N N
vg0221587239 T -> C LOC_Os02g35940.1 upstream_gene_variant ; 528.0bp to feature; MODIFIER silent_mutation Average:89.241; most accessible tissue: Zhenshan97 young leaf, score: 94.425 N N N N
vg0221587239 T -> C LOC_Os02g35930-LOC_Os02g35940 intergenic_region ; MODIFIER silent_mutation Average:89.241; most accessible tissue: Zhenshan97 young leaf, score: 94.425 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)
vg0221587239 T C -0.07 -0.06 -0.09 -0.07 -0.08 -0.05

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0221587239 NA 1.43E-104 mr1008 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
vg0221587239 NA 3.92E-104 mr1009 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
vg0221587239 NA 1.22E-76 mr1014 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
vg0221587239 NA 6.71E-78 mr1015 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
vg0221587239 NA 2.52E-67 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
vg0221587239 NA 1.71E-32 mr1081 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
vg0221587239 NA 3.98E-11 mr1128 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
vg0221587239 NA 2.41E-84 mr1134 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
vg0221587239 NA 3.99E-78 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
vg0221587239 NA 1.56E-43 mr1194 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
vg0221587239 NA 2.93E-23 mr1375 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
vg0221587239 NA 1.13E-92 mr1504 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
vg0221587239 NA 6.28E-86 mr1517 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
vg0221587239 NA 2.80E-13 mr1641 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
vg0221587239 NA 8.66E-08 mr1660 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
vg0221587239 NA 4.65E-36 mr1670 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
vg0221587239 NA 6.07E-87 mr1672 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
vg0221587239 NA 6.70E-36 mr1682 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
vg0221587239 NA 1.01E-60 mr1695 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
vg0221587239 NA 1.14E-10 mr1714 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
vg0221587239 NA 4.97E-19 mr1754 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
vg0221587239 NA 3.65E-18 mr1767 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
vg0221587239 NA 2.13E-10 mr1921 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
vg0221587239 NA 1.48E-104 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
vg0221587239 NA 1.70E-12 mr1128_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
vg0221587239 NA 8.08E-18 mr1416_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
vg0221587239 NA 2.31E-07 mr1683_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
vg0221587239 NA 6.58E-15 mr1767_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