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Detailed information for vg1015773658:

Variant ID: vg1015773658 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 15773658
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GGCGGCCGACCCAGCTACAGCCCGCGTCGCCCCACACCCCCTTGGCCATATCTATTTAAAAATTGTCATATGTAGAAAGCCCACGCGCGACGGCCCATCA[G/A]
TGTCCGCTTCTGTCTCGAGCGCGACGTTTCGTTTCTCTGTTTCTCCCGCATCGCTCGCTCGCCGAGAGAGACAGAAGCCGAGACGTCGGTCGACTTCCTC

Reverse complement sequence

GAGGAAGTCGACCGACGTCTCGGCTTCTGTCTCTCTCGGCGAGCGAGCGATGCGGGAGAAACAGAGAAACGAAACGTCGCGCTCGAGACAGAAGCGGACA[C/T]
TGATGGGCCGTCGCGCGTGGGCTTTCTACATATGACAATTTTTAAATAGATATGGCCAAGGGGGTGTGGGGCGACGCGGGCTGTAGCTGGGTCGGCCGCC

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 90.60% 6.50% 1.12% 1.76% NA
All Indica  2759 99.70% 0.00% 0.22% 0.00% NA
All Japonica  1512 73.10% 19.80% 2.31% 4.76% 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% 0.00% 0.65% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.50% 0.10% 0.38% 0.00% NA
Temperate Japonica  767 97.30% 2.60% 0.00% 0.13% NA
Tropical Japonica  504 31.70% 48.40% 6.75% 13.10% NA
Japonica Intermediate  241 82.60% 14.90% 0.41% 2.07% NA
VI/Aromatic  96 81.20% 0.00% 9.38% 9.38% NA
Intermediate  90 88.90% 5.60% 3.33% 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
vg1015773658 G -> A LOC_Os10g30350.1 upstream_gene_variant ; 1012.0bp to feature; MODIFIER silent_mutation Average:97.328; most accessible tissue: Minghui63 root, score: 98.433 N N N N
vg1015773658 G -> A LOC_Os10g30360.1 upstream_gene_variant ; 912.0bp to feature; MODIFIER silent_mutation Average:97.328; most accessible tissue: Minghui63 root, score: 98.433 N N N N
vg1015773658 G -> A LOC_Os10g30350-LOC_Os10g30360 intergenic_region ; MODIFIER silent_mutation Average:97.328; most accessible tissue: Minghui63 root, score: 98.433 N N N N
vg1015773658 G -> DEL N N silent_mutation Average:97.328; most accessible tissue: Minghui63 root, score: 98.433 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)
vg1015773658 G A -0.1 -0.07 -0.05 -0.04 -0.04 -0.06

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1015773658 NA 6.74E-06 mr1328 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
vg1015773658 NA 2.30E-07 mr1338 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
vg1015773658 9.37E-07 1.00E-14 mr1410 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
vg1015773658 NA 2.07E-11 mr1410 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
vg1015773658 NA 5.14E-07 mr1425 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
vg1015773658 NA 1.93E-06 mr1530 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
vg1015773658 NA 3.19E-06 mr1991 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
vg1015773658 4.54E-08 4.37E-21 mr1301_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
vg1015773658 3.88E-09 1.47E-17 mr1410_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
vg1015773658 NA 1.03E-12 mr1410_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
vg1015773658 NA 1.28E-10 mr1905_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