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Detailed information for vg0200335580:

Variant ID: vg0200335580 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 335580
Reference Allele: AAlternative Allele: T
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 113. )

Flanking Sequence (100 bp) in Reference Genome:


GAGAGAAAAAATATTTTCTTTTTGTTTGTGGTAGAACTTAAGCATAAGGTGTACCCTAAGCTAATGCTACTTTCCACAATATATATGGCTCACTTTACAA[A/T]
TATAATCATTGCCTTAAGGTGTCGTATCGGATGGCTTGCCTACCAATCTGCCTAGTCAGCATCGACCAAAGCACAAACACGTGTCGCGTTGGAATCGATC

Reverse complement sequence

GATCGATTCCAACGCGACACGTGTTTGTGCTTTGGTCGATGCTGACTAGGCAGATTGGTAGGCAAGCCATCCGATACGACACCTTAAGGCAATGATTATA[T/A]
TTGTAAAGTGAGCCATATATATTGTGGAAAGTAGCATTAGCTTAGGGTACACCTTATGCTTAAGTTCTACCACAAACAAAAAGAAAATATTTTTTCTCTC

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 60.20% 35.30% 2.92% 1.57% NA
All Indica  2759 35.60% 56.90% 4.78% 2.68% NA
All Japonica  1512 98.70% 1.30% 0.00% 0.00% NA
Aus  269 94.80% 4.80% 0.37% 0.00% NA
Indica I  595 33.60% 65.40% 1.01% 0.00% NA
Indica II  465 33.30% 59.80% 5.38% 1.51% NA
Indica III  913 35.00% 54.80% 5.48% 4.71% NA
Indica Intermediate  786 39.20% 51.30% 6.49% 3.05% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 97.20% 2.80% 0.00% 0.00% NA
Japonica Intermediate  241 97.90% 2.10% 0.00% 0.00% NA
VI/Aromatic  96 54.20% 44.80% 1.04% 0.00% NA
Intermediate  90 67.80% 27.80% 4.44% 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
vg0200335580 A -> T LOC_Os02g01580-LOC_Os02g01590 intergenic_region ; MODIFIER silent_mutation Average:96.297; most accessible tissue: Minghui63 flower, score: 98.979 N N N N
vg0200335580 A -> DEL N N silent_mutation Average:96.297; most accessible tissue: Minghui63 flower, score: 98.979 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)
vg0200335580 A T -0.02 -0.02 -0.03 -0.02 -0.02 -0.04

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0200335580 NA 1.58E-06 mr1042 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
vg0200335580 NA 2.57E-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
vg0200335580 NA 8.35E-06 mr1043 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
vg0200335580 NA 6.46E-08 mr1059 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
vg0200335580 NA 2.27E-08 mr1167 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
vg0200335580 NA 7.41E-07 mr1291 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
vg0200335580 NA 2.94E-06 mr1479 Ind_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
vg0200335580 NA 4.79E-06 mr1502 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
vg0200335580 NA 1.91E-06 mr1892 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
vg0200335580 NA 4.81E-06 mr1975 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
vg0200335580 NA 1.07E-09 mr1995 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
vg0200335580 NA 2.88E-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
vg0200335580 NA 1.58E-06 mr1892_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
vg0200335580 NA 1.20E-06 mr1892_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