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Detailed information for vg0401023830:

Variant ID: vg0401023830 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 1023830
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.89, A: 0.10, others allele: 0.00, population size: 105. )

Flanking Sequence (100 bp) in Reference Genome:


GGGCGACGGAGATGAGGCCCTCGACGCACTGGTTGAGGATGTCCTCGTCGTCGGTGTAGTCGAAGATGGCGGCGAGGGTGGCGACGGCGGGGCCGGAGAC[G/A]
GTGACGAACACCTCGCGGGTGAGCTTGTGCTTGAAGTCGCAGGGGGTGAAGGGGTCGATGGCGCGGGAGCGCTTGACGAGGTCGGCCCATCTGGTGGGCG

Reverse complement sequence

CGCCCACCAGATGGGCCGACCTCGTCAAGCGCTCCCGCGCCATCGACCCCTTCACCCCCTGCGACTTCAAGCACAAGCTCACCCGCGAGGTGTTCGTCAC[C/T]
GTCTCCGGCCCCGCCGTCGCCACCCTCGCCGCCATCTTCGACTACACCGACGACGAGGACATCCTCAACCAGTGCGTCGAGGGCCTCATCTCCGTCGCCC

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 94.40% 5.60% 0.04% 0.00% NA
All Indica  2759 97.80% 2.10% 0.07% 0.00% NA
All Japonica  1512 90.70% 9.30% 0.00% 0.00% NA
Aus  269 97.80% 2.20% 0.00% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 97.20% 2.40% 0.43% 0.00% NA
Indica III  913 95.60% 4.40% 0.00% 0.00% NA
Indica Intermediate  786 99.10% 0.90% 0.00% 0.00% NA
Temperate Japonica  767 93.20% 6.80% 0.00% 0.00% NA
Tropical Japonica  504 91.50% 8.50% 0.00% 0.00% NA
Japonica Intermediate  241 81.30% 18.70% 0.00% 0.00% NA
VI/Aromatic  96 46.90% 53.10% 0.00% 0.00% NA
Intermediate  90 92.20% 7.80% 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
vg0401023830 G -> A LOC_Os04g02680.1 upstream_gene_variant ; 4136.0bp to feature; MODIFIER silent_mutation Average:83.553; most accessible tissue: Zhenshan97 young leaf, score: 92.976 N N N N
vg0401023830 G -> A LOC_Os04g02690.1 downstream_gene_variant ; 301.0bp to feature; MODIFIER silent_mutation Average:83.553; most accessible tissue: Zhenshan97 young leaf, score: 92.976 N N N N
vg0401023830 G -> A LOC_Os04g02680-LOC_Os04g02690 intergenic_region ; MODIFIER silent_mutation Average:83.553; most accessible tissue: Zhenshan97 young leaf, score: 92.976 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)
vg0401023830 G A -0.01 -0.01 -0.02 -0.01 -0.01 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0401023830 3.12E-06 4.73E-06 mr1829 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
vg0401023830 5.00E-07 1.51E-06 mr1829_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
vg0401023830 1.89E-06 5.32E-07 mr1842_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