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Detailed information for vg0620057031:

Variant ID: vg0620057031 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 20057031
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.76, T: 0.24, others allele: 0.00, population size: 63. )

Flanking Sequence (100 bp) in Reference Genome:


TGCGCACTCCATGTCGCCACCACCACGCTATGCATTAACCGCCGCTACACTGTCCGCTTCCAATCCACCACCTTCAGTGCTCAATCGACCAAGCCGCCAC[T/C]
ACCCCCAAGCTCCTTGTCCCTCTGTGACCCTATTTCACTCCTCACCAGTGCCCAACGACCACCGCCGCCATTTTCTCTAAATCCGGCCACCACCGCCACT

Reverse complement sequence

AGTGGCGGTGGTGGCCGGATTTAGAGAAAATGGCGGCGGTGGTCGTTGGGCACTGGTGAGGAGTGAAATAGGGTCACAGAGGGACAAGGAGCTTGGGGGT[A/G]
GTGGCGGCTTGGTCGATTGAGCACTGAAGGTGGTGGATTGGAAGCGGACAGTGTAGCGGCGGTTAATGCATAGCGTGGTGGTGGCGACATGGAGTGCGCA

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 73.40% 26.60% 0.04% 0.00% NA
All Indica  2759 95.40% 4.60% 0.00% 0.00% NA
All Japonica  1512 26.90% 72.90% 0.13% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 95.00% 5.00% 0.00% 0.00% NA
Indica II  465 94.00% 6.00% 0.00% 0.00% NA
Indica III  913 99.50% 0.50% 0.00% 0.00% NA
Indica Intermediate  786 92.00% 8.00% 0.00% 0.00% NA
Temperate Japonica  767 14.90% 85.00% 0.13% 0.00% NA
Tropical Japonica  504 30.40% 69.40% 0.20% 0.00% NA
Japonica Intermediate  241 58.10% 41.90% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 71.10% 28.90% 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
vg0620057031 T -> C LOC_Os06g34460.1 splice_region_variant&intron_variant ; LOW silent_mutation Average:84.727; most accessible tissue: Zhenshan97 young leaf, score: 92.818 N N N N
vg0620057031 T -> C LOC_Os06g34450.1 downstream_gene_variant ; 4533.0bp to feature; MODIFIER silent_mutation Average:84.727; most accessible tissue: Zhenshan97 young leaf, score: 92.818 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)
vg0620057031 T C 0.01 0.0 0.0 0.01 0.01 0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0620057031 NA 7.38E-07 mr1245 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
vg0620057031 NA 1.78E-09 mr1336 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
vg0620057031 NA 1.20E-06 mr1527 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
vg0620057031 NA 3.45E-06 mr1532 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
vg0620057031 NA 3.17E-07 mr1690 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
vg0620057031 NA 3.96E-14 mr1726 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
vg0620057031 5.98E-09 9.03E-11 mr1165_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
vg0620057031 5.41E-06 5.42E-06 mr1971_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