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Detailed information for vg0316626378:

Variant ID: vg0316626378 (JBrowse)Variation Type: INDEL
Chromosome: chr03Position: 16626378
Reference Allele: AAlternative Allele: G,AG
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ACACGGCCGGGCGAGCATATTTACGCGGAATATGCCTCGAAACCGTCCTTGCGCCGTTTAAGACGAGTGGAAGCAGCCAAAAAAAAAAAACAGAGAGAGA[A/G,AG]
AGAAAGACCAAGGAAGACTTGACTCACCTGCAAGTATTGGGCTAGTGGCTAATGAAGTTCATACACACACGTGACAAACTACCCATCGACCACATGGTTG

Reverse complement sequence

CAACCATGTGGTCGATGGGTAGTTTGTCACGTGTGTGTATGAACTTCATTAGCCACTAGCCCAATACTTGCAGGTGAGTCAAGTCTTCCTTGGTCTTTCT[T/C,CT]
TCTCTCTCTGTTTTTTTTTTTTGGCTGCTTCCACTCGTCTTAAACGGCGCAAGGACGGTTTCGAGGCATATTCCGCGTAAATATGCTCGCCCGGCCGTGT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 52.20% 47.20% 0.47% 0.00% AG: 0.06%
All Indica  2759 25.70% 73.50% 0.69% 0.00% AG: 0.11%
All Japonica  1512 90.40% 9.50% 0.07% 0.00% NA
Aus  269 91.40% 8.60% 0.00% 0.00% NA
Indica I  595 43.50% 55.50% 1.01% 0.00% NA
Indica II  465 9.20% 90.10% 0.43% 0.00% AG: 0.22%
Indica III  913 23.00% 76.10% 0.77% 0.00% AG: 0.11%
Indica Intermediate  786 25.20% 74.20% 0.51% 0.00% AG: 0.13%
Temperate Japonica  767 96.90% 3.10% 0.00% 0.00% NA
Tropical Japonica  504 95.60% 4.40% 0.00% 0.00% NA
Japonica Intermediate  241 58.90% 40.70% 0.41% 0.00% NA
VI/Aromatic  96 92.70% 7.30% 0.00% 0.00% NA
Intermediate  90 62.20% 35.60% 2.22% 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
vg0316626378 A -> AG LOC_Os03g29230.1 upstream_gene_variant ; 1459.0bp to feature; MODIFIER silent_mutation Average:76.748; most accessible tissue: Callus, score: 94.84 N N N N
vg0316626378 A -> AG LOC_Os03g29240.1 upstream_gene_variant ; 2167.0bp to feature; MODIFIER silent_mutation Average:76.748; most accessible tissue: Callus, score: 94.84 N N N N
vg0316626378 A -> AG LOC_Os03g29224.1 downstream_gene_variant ; 2596.0bp to feature; MODIFIER silent_mutation Average:76.748; most accessible tissue: Callus, score: 94.84 N N N N
vg0316626378 A -> AG LOC_Os03g29230-LOC_Os03g29240 intergenic_region ; MODIFIER silent_mutation Average:76.748; most accessible tissue: Callus, score: 94.84 N N N N
vg0316626378 A -> G LOC_Os03g29230.1 upstream_gene_variant ; 1458.0bp to feature; MODIFIER silent_mutation Average:76.748; most accessible tissue: Callus, score: 94.84 N N N N
vg0316626378 A -> G LOC_Os03g29240.1 upstream_gene_variant ; 2168.0bp to feature; MODIFIER silent_mutation Average:76.748; most accessible tissue: Callus, score: 94.84 N N N N
vg0316626378 A -> G LOC_Os03g29224.1 downstream_gene_variant ; 2595.0bp to feature; MODIFIER silent_mutation Average:76.748; most accessible tissue: Callus, score: 94.84 N N N N
vg0316626378 A -> G LOC_Os03g29230-LOC_Os03g29240 intergenic_region ; MODIFIER silent_mutation Average:76.748; most accessible tissue: Callus, score: 94.84 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)
vg0316626378 A AG -0.3 0.09 0.04 0.02 -0.02 -0.03
vg0316626378 A G 0.04 0.07 0.04 0.06 0.07 0.05

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0316626378 7.69E-06 NA mr1101 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
vg0316626378 NA 2.62E-06 mr1114 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
vg0316626378 NA 1.87E-06 mr1117 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
vg0316626378 NA 3.58E-06 mr1123 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
vg0316626378 NA 5.34E-06 mr1242 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
vg0316626378 NA 2.30E-06 mr1247 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
vg0316626378 NA 2.85E-06 mr1496 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
vg0316626378 NA 1.41E-06 mr1961 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
vg0316626378 NA 1.91E-06 mr1113_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
vg0316626378 NA 1.36E-07 mr1114_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
vg0316626378 NA 1.91E-08 mr1117_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
vg0316626378 NA 5.63E-06 mr1118_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
vg0316626378 NA 2.78E-07 mr1119_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
vg0316626378 NA 1.07E-06 mr1120_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
vg0316626378 NA 5.38E-07 mr1123_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
vg0316626378 5.54E-07 NA mr1150_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
vg0316626378 3.28E-07 2.13E-10 mr1240_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
vg0316626378 NA 4.29E-07 mr1242_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
vg0316626378 NA 1.29E-07 mr1247_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
vg0316626378 NA 7.51E-09 mr1496_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
vg0316626378 NA 8.49E-06 mr1936_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
vg0316626378 NA 2.55E-07 mr1961_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