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Detailed information for vg0716828374:

Variant ID: vg0716828374 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 16828374
Reference Allele: CAlternative Allele: A,T
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CACCACCTAACTCACCAACATCCTAACACTCGAAAGCAAACAAAGGCATGCATTTACATCCCACCAACGATGTAAACACATGCAAGACCCACACACACAA[C/A,T]
CAAACTTAAGCAAGCAAACTAACATAACGATCTAAGACAACGACTTAGCAAAACGGTCTAGGTCTTCCGGGCATCGGAGTTGATTGAAGGCTCATTCGGC

Reverse complement sequence

GCCGAATGAGCCTTCAATCAACTCCGATGCCCGGAAGACCTAGACCGTTTTGCTAAGTCGTTGTCTTAGATCGTTATGTTAGTTTGCTTGCTTAAGTTTG[G/T,A]
TTGTGTGTGTGGGTCTTGCATGTGTTTACATCGTTGGTGGGATGTAAATGCATGCCTTTGTTTGCTTTCGAGTGTTAGGATGTTGGTGAGTTAGGTGGTG

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 79.60% 10.50% 7.30% 2.67% NA
All Indica  2759 65.90% 17.80% 12.21% 4.10% NA
All Japonica  1512 99.10% 0.00% 0.26% 0.66% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 95.80% 1.20% 3.03% 0.00% NA
Indica II  465 38.30% 17.00% 34.19% 10.54% NA
Indica III  913 53.50% 33.10% 9.42% 4.05% NA
Indica Intermediate  786 73.90% 13.20% 9.41% 3.44% NA
Temperate Japonica  767 98.30% 0.00% 0.39% 1.30% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.00% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 88.90% 3.30% 4.44% 3.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0716828374 C -> DEL N N silent_mutation Average:57.23; most accessible tissue: Zhenshan97 flag leaf, score: 88.445 N N N N
vg0716828374 C -> A LOC_Os07g28760.1 upstream_gene_variant ; 4904.0bp to feature; MODIFIER silent_mutation Average:57.23; most accessible tissue: Zhenshan97 flag leaf, score: 88.445 N N N N
vg0716828374 C -> A LOC_Os07g28750.1 intron_variant ; MODIFIER silent_mutation Average:57.23; most accessible tissue: Zhenshan97 flag leaf, score: 88.445 N N N N
vg0716828374 C -> T LOC_Os07g28760.1 upstream_gene_variant ; 4904.0bp to feature; MODIFIER N Average:57.23; most accessible tissue: Zhenshan97 flag leaf, score: 88.445 N N N N
vg0716828374 C -> T LOC_Os07g28750.1 intron_variant ; MODIFIER N Average:57.23; most accessible tissue: Zhenshan97 flag leaf, score: 88.445 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)
vg0716828374 C A 0.0 0.0 0.0 -0.01 -0.01 -0.02
vg0716828374 C T 0.0 0.0 -0.01 -0.01 -0.01 -0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0716828374 9.57E-07 8.02E-11 mr1113 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
vg0716828374 3.07E-06 9.51E-10 mr1114 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
vg0716828374 NA 2.54E-09 mr1116 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
vg0716828374 NA 1.57E-06 mr1117 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
vg0716828374 2.84E-06 1.99E-15 mr1118 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
vg0716828374 NA 3.51E-09 mr1119 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
vg0716828374 9.24E-06 1.09E-07 mr1120 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
vg0716828374 4.80E-06 2.74E-14 mr1183 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
vg0716828374 NA 9.51E-09 mr1183 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
vg0716828374 9.86E-08 6.34E-11 mr1247 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
vg0716828374 7.74E-07 4.19E-19 mr1495 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
vg0716828374 9.57E-06 5.74E-13 mr1503 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
vg0716828374 NA 7.38E-08 mr1503 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
vg0716828374 NA 5.76E-13 mr1794 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
vg0716828374 NA 4.38E-10 mr1794 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
vg0716828374 NA 2.82E-06 mr1842 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
vg0716828374 NA 4.73E-07 mr1917 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
vg0716828374 NA 9.18E-06 mr1936 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
vg0716828374 NA 2.52E-11 mr1113_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
vg0716828374 NA 6.47E-12 mr1114_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
vg0716828374 NA 5.60E-09 mr1117_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
vg0716828374 NA 3.84E-15 mr1118_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
vg0716828374 NA 2.36E-09 mr1119_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
vg0716828374 NA 6.74E-11 mr1120_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
vg0716828374 NA 7.10E-10 mr1247_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
vg0716828374 5.19E-07 NA mr1258_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
vg0716828374 7.21E-07 4.02E-09 mr1258_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
vg0716828374 NA 1.01E-17 mr1495_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
vg0716828374 NA 2.17E-08 mr1613_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
vg0716828374 NA 4.10E-07 mr1619_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
vg0716828374 NA 3.44E-06 mr1866_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