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Detailed information for vg0723183493:

Variant ID: vg0723183493 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 23183493
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: 286. )

Flanking Sequence (100 bp) in Reference Genome:


CACAGCCATGGCCGTAGTAGCTCACGAGCACTCACCAAGCTGTCTCAAAAGGGCTATAGAAAGAAAACAAGCTGCCTTCACATGCCACACAGGGGCCCCT[G/A]
CTTTTCTTTTGGTTGGATTCGATGGAAAATAATTACACCAACAAAATCCAGTCCCAAATTTTTTTCCCAAAAACATCATATCGAATCTTTAGACACATAC

Reverse complement sequence

GTATGTGTCTAAAGATTCGATATGATGTTTTTGGGAAAAAAATTTGGGACTGGATTTTGTTGGTGTAATTATTTTCCATCGAATCCAACCAAAAGAAAAG[C/T]
AGGGGCCCCTGTGTGGCATGTGAAGGCAGCTTGTTTTCTTTCTATAGCCCTTTTGAGACAGCTTGGTGAGTGCTCGTGAGCTACTACGGCCATGGCTGTG

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 93.50% 6.50% 0.02% 0.00% NA
All Indica  2759 99.70% 0.30% 0.00% 0.00% NA
All Japonica  1512 83.90% 16.00% 0.07% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.40% 0.60% 0.00% 0.00% NA
Indica III  913 99.70% 0.30% 0.00% 0.00% NA
Indica Intermediate  786 99.70% 0.30% 0.00% 0.00% NA
Temperate Japonica  767 83.60% 16.40% 0.00% 0.00% NA
Tropical Japonica  504 85.90% 14.10% 0.00% 0.00% NA
Japonica Intermediate  241 80.90% 18.70% 0.41% 0.00% NA
VI/Aromatic  96 47.90% 52.10% 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
vg0723183493 G -> A LOC_Os07g38590.1 downstream_gene_variant ; 686.0bp to feature; MODIFIER silent_mutation Average:79.324; most accessible tissue: Zhenshan97 panicle, score: 98.13 N N N N
vg0723183493 G -> A LOC_Os07g38600.1 downstream_gene_variant ; 1812.0bp to feature; MODIFIER silent_mutation Average:79.324; most accessible tissue: Zhenshan97 panicle, score: 98.13 N N N N
vg0723183493 G -> A LOC_Os07g38610.1 downstream_gene_variant ; 3799.0bp to feature; MODIFIER silent_mutation Average:79.324; most accessible tissue: Zhenshan97 panicle, score: 98.13 N N N N
vg0723183493 G -> A LOC_Os07g38590-LOC_Os07g38600 intergenic_region ; MODIFIER silent_mutation Average:79.324; most accessible tissue: Zhenshan97 panicle, score: 98.13 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)
vg0723183493 G A 0.02 0.0 -0.02 -0.03 0.01 0.04

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0723183493 NA 5.43E-22 Awn_length All Not 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
vg0723183493 NA 4.09E-11 Awn_length Jap_All Not 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
vg0723183493 NA 1.43E-06 mr1138 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
vg0723183493 8.52E-08 2.53E-10 mr1354 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
vg0723183493 NA 2.40E-08 mr1354 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
vg0723183493 NA 2.31E-11 mr1829 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
vg0723183493 NA 4.61E-07 mr1057_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
vg0723183493 6.54E-07 NA mr1354_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
vg0723183493 NA 1.92E-07 mr1354_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
vg0723183493 NA 7.50E-07 mr1549_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
vg0723183493 NA 2.09E-06 mr1757_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
vg0723183493 1.00E-08 4.34E-18 mr1829_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
vg0723183493 NA 9.65E-07 mr1829_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
vg0723183493 NA 7.44E-19 mr1842_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
vg0723183493 1.10E-08 1.03E-20 mr1902_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
vg0723183493 NA 1.83E-06 mr1902_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