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Detailed information for vg0729061858:

Variant ID: vg0729061858 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 29061858
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GGTGTGTTTAGTTCACGCTAAAATTGAATGTTTGATTGAAATTAGAACGATGTGACGAAAAAGTTAGAAGTTTGTGCGTGTAGAAAAGTTTTGATGTGAT[C/T]
GAAAAGTTGGAAACTAAACCAGACCTATGGCTCCAATTCAACTGAGTTTTTTTTCCCTTACAAGGCTCCTCGTGTCCTTCAGAGAGCACGGGTGTCTTGT

Reverse complement sequence

ACAAGACACCCGTGCTCTCTGAAGGACACGAGGAGCCTTGTAAGGGAAAAAAAACTCAGTTGAATTGGAGCCATAGGTCTGGTTTAGTTTCCAACTTTTC[G/A]
ATCACATCAAAACTTTTCTACACGCACAAACTTCTAACTTTTTCGTCACATCGTTCTAATTTCAATCAAACATTCAATTTTAGCGTGAACTAAACACACC

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 80.30% 1.00% 11.91% 6.75% NA
All Indica  2759 73.20% 0.00% 16.93% 9.89% NA
All Japonica  1512 92.10% 3.10% 3.31% 1.52% NA
Aus  269 80.30% 0.00% 12.27% 7.43% NA
Indica I  595 61.20% 0.00% 32.94% 5.88% NA
Indica II  465 69.20% 0.00% 18.92% 11.83% NA
Indica III  913 81.10% 0.00% 7.23% 11.72% NA
Indica Intermediate  786 75.40% 0.00% 14.89% 9.67% NA
Temperate Japonica  767 92.60% 5.60% 1.43% 0.39% NA
Tropical Japonica  504 94.80% 0.00% 2.18% 2.98% NA
Japonica Intermediate  241 84.60% 1.70% 11.62% 2.07% NA
VI/Aromatic  96 95.80% 0.00% 1.04% 3.12% NA
Intermediate  90 85.60% 1.10% 13.33% 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
vg0729061858 C -> DEL N N silent_mutation Average:71.429; most accessible tissue: Minghui63 panicle, score: 94.558 N N N N
vg0729061858 C -> T LOC_Os07g48550-LOC_Os07g48560 intergenic_region ; MODIFIER silent_mutation Average:71.429; most accessible tissue: Minghui63 panicle, score: 94.558 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)
vg0729061858 C T 0.02 0.0 0.0 0.03 0.03 0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0729061858 NA 1.37E-09 mr1757 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
vg0729061858 3.37E-10 3.71E-13 mr1549_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
vg0729061858 3.80E-06 3.34E-07 mr1550_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
vg0729061858 2.78E-07 1.48E-10 mr1757_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