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Detailed information for vg1003340833:

Variant ID: vg1003340833 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 3340833
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.88, T: 0.12, others allele: 0.00, population size: 49. )

Flanking Sequence (100 bp) in Reference Genome:


GGCGTCGGCGCACCAAGCAGTCCTAGAGCTCCTACACCACCACCAAATACGGCGCAGAGCTCGCGGATGGCGTGGAGACGGTGGAGGCGACAGCGATAGG[C/T]
GCAGGAGCGCCGAGGGATAGCATATGATCCTCTCGATCCTGGGGCTCGCCAGGATAGTAGCGGCCTCGGCGTGTGCTGGGTTTCTCGGGCACGTCGGGAT

Reverse complement sequence

ATCCCGACGTGCCCGAGAAACCCAGCACACGCCGAGGCCGCTACTATCCTGGCGAGCCCCAGGATCGAGAGGATCATATGCTATCCCTCGGCGCTCCTGC[G/A]
CCTATCGCTGTCGCCTCCACCGTCTCCACGCCATCCGCGAGCTCTGCGCCGTATTTGGTGGTGGTGTAGGAGCTCTAGGACTGCTTGGTGCGCCGACGCC

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 82.30% 8.70% 0.68% 8.32% NA
All Indica  2759 70.10% 14.80% 1.09% 13.99% NA
All Japonica  1512 99.70% 0.00% 0.13% 0.20% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 75.30% 16.50% 0.84% 7.39% NA
Indica II  465 71.20% 13.80% 0.65% 14.41% NA
Indica III  913 69.10% 15.80% 0.99% 14.13% NA
Indica Intermediate  786 66.70% 13.10% 1.65% 18.58% NA
Temperate Japonica  767 99.90% 0.00% 0.00% 0.13% NA
Tropical Japonica  504 99.20% 0.00% 0.40% 0.40% 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 92.20% 3.30% 0.00% 4.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1003340833 C -> T LOC_Os10g06500.1 missense_variant ; p.Arg56His; MODERATE nonsynonymous_codon ; R56H Average:78.767; most accessible tissue: Zhenshan97 flag leaf, score: 89.211 unknown unknown TOLERATED 0.37
vg1003340833 C -> DEL LOC_Os10g06500.1 N frameshift_variant Average:78.767; most accessible tissue: Zhenshan97 flag leaf, score: 89.211 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)
vg1003340833 C T 0.0 0.0 0.0 0.0 0.0 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1003340833 NA 5.10E-07 mr1538 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
vg1003340833 7.76E-10 1.22E-09 mr1547 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
vg1003340833 4.30E-08 3.65E-10 mr1547 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
vg1003340833 1.96E-13 8.53E-15 mr1709 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
vg1003340833 3.21E-11 4.12E-12 mr1709 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
vg1003340833 NA 9.34E-06 mr1015_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
vg1003340833 NA 2.46E-07 mr1538_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
vg1003340833 1.96E-09 4.55E-11 mr1547_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
vg1003340833 2.34E-09 5.09E-13 mr1547_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
vg1003340833 1.59E-20 1.75E-15 mr1709_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
vg1003340833 1.12E-14 3.79E-13 mr1709_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