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Detailed information for vg0803657241:

Variant ID: vg0803657241 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 3657241
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AGCAGAGGCTGAGGACAGAGCATGCAGGCAGTGGCCATGCTCCCCCCAGGGCCGTACGTTAACACAGCCCCCAGGGTGGCATTTCGCTACACGGCACCCG[G/A]
GCCTTGCCATCAACGTTGTCAGGACCCGGATCCTAGCCAGTATCATATAATAGTATCGGGATCCTATGAGAATTTTTTTAACTTTAATTAATTACATATA

Reverse complement sequence

TATATGTAATTAATTAAAGTTAAAAAAATTCTCATAGGATCCCGATACTATTATATGATACTGGCTAGGATCCGGGTCCTGACAACGTTGATGGCAAGGC[C/T]
CGGGTGCCGTGTAGCGAAATGCCACCCTGGGGGCTGTGTTAACGTACGGCCCTGGGGGGAGCATGGCCACTGCCTGCATGCTCTGTCCTCAGCCTCTGCT

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 83.90% 14.90% 1.23% 0.00% NA
All Indica  2759 99.70% 0.10% 0.11% 0.00% NA
All Japonica  1512 50.60% 45.80% 3.57% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 99.10% 0.20% 0.65% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.70% 0.30% 0.00% 0.00% NA
Temperate Japonica  767 51.50% 42.80% 5.74% 0.00% NA
Tropical Japonica  504 54.20% 45.20% 0.60% 0.00% NA
Japonica Intermediate  241 40.20% 56.80% 2.90% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 93.30% 5.60% 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
vg0803657241 G -> A LOC_Os08g06478.1 downstream_gene_variant ; 34.0bp to feature; MODIFIER silent_mutation Average:99.788; most accessible tissue: Minghui63 panicle, score: 99.905 N N N N
vg0803657241 G -> A LOC_Os08g06474-LOC_Os08g06478 intergenic_region ; MODIFIER silent_mutation Average:99.788; most accessible tissue: Minghui63 panicle, score: 99.905 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)
vg0803657241 G A -0.03 -0.06 -0.04 -0.05 -0.03 -0.03

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0803657241 1.55E-09 NA mr1182 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
vg0803657241 9.42E-06 2.72E-06 mr1182 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
vg0803657241 8.42E-10 NA mr1282 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
vg0803657241 3.09E-06 4.10E-07 mr1282 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
vg0803657241 NA 2.42E-09 mr1624 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
vg0803657241 5.41E-09 NA mr1650 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
vg0803657241 4.34E-06 4.85E-06 mr1650 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
vg0803657241 7.32E-09 NA mr1658 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
vg0803657241 NA 2.53E-06 mr1658 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
vg0803657241 2.25E-07 NA mr1182_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
vg0803657241 1.45E-07 NA mr1282_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
vg0803657241 NA 1.37E-06 mr1282_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
vg0803657241 2.53E-07 1.76E-11 mr1624_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
vg0803657241 3.80E-06 1.96E-07 mr1624_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