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Detailed information for vg0618029961:

Variant ID: vg0618029961 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 18029961
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 322. )

Flanking Sequence (100 bp) in Reference Genome:


CTTCCTTGCCCCGGAGTATTTCGCCCAAAGGGTACTGTGATGGCACCGTGACTTTGTGGGCCTGAAAGTAATGTTTAAGCTTGCGCGAAGCCATCACCAG[G/A]
GCGTAAGCAAGCTTCTCCATTTCAATGTATCTTATCTTTGCTCCATGCAAGGCTTCGGAGACGAAATAAACTGGTTTCTTGCCTGACTCTGTCTCTTGGA

Reverse complement sequence

TCCAAGAGACAGAGTCAGGCAAGAAACCAGTTTATTTCGTCTCCGAAGCCTTGCATGGAGCAAAGATAAGATACATTGAAATGGAGAAGCTTGCTTACGC[C/T]
CTGGTGATGGCTTCGCGCAAGCTTAAACATTACTTTCAGGCCCACAAAGTCACGGTGCCATCACAGTACCCTTTGGGCGAAATACTCCGGGGCAAGGAAG

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 93.40% 6.30% 0.36% 0.00% NA
All Indica  2759 89.80% 9.60% 0.62% 0.00% NA
All Japonica  1512 99.50% 0.50% 0.00% 0.00% NA
Aus  269 92.90% 7.10% 0.00% 0.00% NA
Indica I  595 88.20% 11.10% 0.67% 0.00% NA
Indica II  465 99.10% 0.90% 0.00% 0.00% NA
Indica III  913 85.70% 13.30% 1.10% 0.00% NA
Indica Intermediate  786 90.20% 9.40% 0.38% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 98.80% 1.20% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 97.90% 2.10% 0.00% 0.00% NA
Intermediate  90 97.80% 2.20% 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
vg0618029961 G -> A LOC_Os06g30990.1 synonymous_variant ; p.Ala230Ala; LOW synonymous_codon Average:82.598; most accessible tissue: Minghui63 flag leaf, score: 94.759 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)
vg0618029961 G A -0.01 -0.02 -0.01 -0.01 -0.01 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0618029961 1.30E-06 NA Plant_height Ind_All YES Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0618029961 NA 8.14E-06 mr1043 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
vg0618029961 NA 9.81E-06 mr1277_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
vg0618029961 NA 6.48E-06 mr1291_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
vg0618029961 NA 8.13E-06 mr1291_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
vg0618029961 NA 1.78E-07 mr1925_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