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Detailed information for vg0723923647:

Variant ID: vg0723923647 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 23923647
Reference Allele: CAlternative Allele: T,A
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 120. )

Flanking Sequence (100 bp) in Reference Genome:


AGGGGAGTAGCAACGGCTGCACTCAAGAGCTCTTCTTCGGCAGAGGCAATGACGCTCGCGGCCTACGGCGGCAGCTTTGTCTCACCCATCGAATCCTTGA[C/T,A]
AGTTGCGGTGGCGCTTGTGAACGGAGCAGCGACAACAACAACATTTGTGGGAAGGTTTGCCAGCGCGCGGCGGGGGGGGGGGGGGAGGGTGGAGAGAGAG

Reverse complement sequence

CTCTCTCTCCACCCTCCCCCCCCCCCCCCGCCGCGCGCTGGCAAACCTTCCCACAAATGTTGTTGTTGTCGCTGCTCCGTTCACAAGCGCCACCGCAACT[G/A,T]
TCAAGGATTCGATGGGTGAGACAAAGCTGCCGCCGTAGGCCGCGAGCGTCATTGCCTCTGCCGAAGAAGAGCTCTTGAGTGCAGCCGTTGCTACTCCCCT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 54.60% 44.90% 0.19% 0.30% A: 0.02%
All Indica  2759 27.50% 71.90% 0.14% 0.43% NA
All Japonica  1512 99.70% 0.10% 0.20% 0.00% NA
Aus  269 56.50% 43.50% 0.00% 0.00% NA
Indica I  595 12.30% 87.40% 0.00% 0.34% NA
Indica II  465 31.60% 67.50% 0.22% 0.65% NA
Indica III  913 26.40% 73.30% 0.33% 0.00% NA
Indica Intermediate  786 38.00% 61.10% 0.00% 0.89% NA
Temperate Japonica  767 99.90% 0.00% 0.13% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 98.30% 0.80% 0.83% 0.00% NA
VI/Aromatic  96 99.00% 0.00% 0.00% 0.00% A: 1.04%
Intermediate  90 75.60% 20.00% 2.22% 2.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0723923647 C -> DEL LOC_Os07g39890.1 N frameshift_variant Average:82.989; most accessible tissue: Minghui63 panicle, score: 93.176 N N N N
vg0723923647 C -> A LOC_Os07g39890.1 missense_variant ; p.Val39Phe; MODERATE nonsynonymous_codon ; V39F Average:82.989; most accessible tissue: Minghui63 panicle, score: 93.176 unknown unknown DELETERIOUS 0.04
vg0723923647 C -> T LOC_Os07g39890.1 missense_variant ; p.Val39Ile; MODERATE nonsynonymous_codon ; V39I Average:82.989; most accessible tissue: Minghui63 panicle, score: 93.176 unknown unknown TOLERATED 0.37

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)
vg0723923647 C A 0.01 0.01 0.01 0.0 0.01 0.01
vg0723923647 C T 0.0 0.0 0.01 -0.01 0.0 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0723923647 5.11E-06 NA mr1175 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
vg0723923647 9.41E-08 9.41E-08 mr1175 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
vg0723923647 NA 9.07E-06 mr1186 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
vg0723923647 NA 5.71E-09 mr1352 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
vg0723923647 NA 9.28E-09 mr1215_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
vg0723923647 NA 2.62E-07 mr1215_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
vg0723923647 NA 1.51E-21 mr1218_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
vg0723923647 NA 1.33E-09 mr1218_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
vg0723923647 NA 5.17E-10 mr1220_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
vg0723923647 NA 1.44E-07 mr1220_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
vg0723923647 NA 4.01E-07 mr1422_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
vg0723923647 NA 3.87E-14 mr1521_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
vg0723923647 NA 5.26E-06 mr1521_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
vg0723923647 NA 2.84E-07 mr1583_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
vg0723923647 NA 3.38E-08 mr1607_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
vg0723923647 NA 9.52E-07 mr1607_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
vg0723923647 NA 1.18E-09 mr1646_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
vg0723923647 NA 7.00E-06 mr1844_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
vg0723923647 NA 4.20E-06 mr1954_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
vg0723923647 9.39E-06 9.39E-06 mr1967_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