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Detailed information for vg0625163806:

Variant ID: vg0625163806 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 25163806
Reference Allele: CAlternative Allele: T
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 213. )

Flanking Sequence (100 bp) in Reference Genome:


AGGAAGGGCATCCCCCACCGTGCACCCTTCTACGGTTAGCTCACACACTACACCAACCAAAAAAAAAATTATCACCCATCACCAGCATATACTAGTCTGT[C/T]
CTTAAAAAAAGCAAACTCTAGCTACGATTCTAGACATATCGTAGCTAGGATTGTAATTTTTTTTGGACGGAAGGGGTATATCACTAGCTCTTCAGCCAAA

Reverse complement sequence

TTTGGCTGAAGAGCTAGTGATATACCCCTTCCGTCCAAAAAAAATTACAATCCTAGCTACGATATGTCTAGAATCGTAGCTAGAGTTTGCTTTTTTTAAG[G/A]
ACAGACTAGTATATGCTGGTGATGGGTGATAATTTTTTTTTTGGTTGGTGTAGTGTGTGAGCTAACCGTAGAAGGGTGCACGGTGGGGGATGCCCTTCCT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 59.50% 40.40% 0.11% 0.00% NA
All Indica  2759 95.30% 4.60% 0.11% 0.00% NA
All Japonica  1512 0.80% 99.20% 0.00% 0.00% NA
Aus  269 48.30% 51.30% 0.37% 0.00% NA
Indica I  595 99.80% 0.00% 0.17% 0.00% NA
Indica II  465 93.80% 6.00% 0.22% 0.00% NA
Indica III  913 97.30% 2.70% 0.00% 0.00% NA
Indica Intermediate  786 90.30% 9.50% 0.13% 0.00% NA
Temperate Japonica  767 1.00% 99.00% 0.00% 0.00% NA
Tropical Japonica  504 0.80% 99.20% 0.00% 0.00% NA
Japonica Intermediate  241 0.00% 100.00% 0.00% 0.00% NA
VI/Aromatic  96 2.10% 97.90% 0.00% 0.00% NA
Intermediate  90 45.60% 53.30% 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
vg0625163806 C -> T LOC_Os06g41930.1 3_prime_UTR_variant ; 62.0bp to feature; MODIFIER silent_mutation Average:91.474; most accessible tissue: Minghui63 flag leaf, score: 96.348 N N N N
vg0625163806 C -> T LOC_Os06g41930.3 3_prime_UTR_variant ; 62.0bp to feature; MODIFIER silent_mutation Average:91.474; most accessible tissue: Minghui63 flag leaf, score: 96.348 N N N N
vg0625163806 C -> T LOC_Os06g41930.4 3_prime_UTR_variant ; 62.0bp to feature; MODIFIER silent_mutation Average:91.474; most accessible tissue: Minghui63 flag leaf, score: 96.348 N N N N
vg0625163806 C -> T LOC_Os06g41930.2 3_prime_UTR_variant ; 62.0bp to feature; MODIFIER silent_mutation Average:91.474; most accessible tissue: Minghui63 flag leaf, score: 96.348 N N N N
vg0625163806 C -> T LOC_Os06g41930.5 3_prime_UTR_variant ; 62.0bp to feature; MODIFIER silent_mutation Average:91.474; most accessible tissue: Minghui63 flag leaf, score: 96.348 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)
vg0625163806 C T -0.05 -0.05 -0.04 -0.08 -0.08 -0.05

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0625163806 NA 1.79E-43 mr1064 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
vg0625163806 NA 4.66E-44 mr1092 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
vg0625163806 NA 9.73E-47 mr1534 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
vg0625163806 NA 1.37E-07 mr1604 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
vg0625163806 NA 8.49E-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
vg0625163806 NA 5.10E-07 mr1824 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
vg0625163806 NA 5.31E-07 mr1886 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
vg0625163806 NA 3.05E-66 mr1064_2 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
vg0625163806 NA 2.30E-31 mr1085_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
vg0625163806 NA 3.90E-66 mr1103_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
vg0625163806 NA 5.78E-56 mr1124_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
vg0625163806 NA 8.19E-42 mr1145_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
vg0625163806 NA 7.62E-41 mr1226_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
vg0625163806 NA 3.32E-26 mr1323_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
vg0625163806 NA 1.39E-08 mr1600_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
vg0625163806 NA 6.19E-07 mr1623_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
vg0625163806 NA 1.85E-08 mr1660_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
vg0625163806 NA 1.52E-35 mr1878_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