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Detailed information for vg0721444659:

Variant ID: vg0721444659 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 21444659
Reference Allele: CAlternative Allele: T
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AGACGGCGTCCGGGCCGACGCCGCGGACGCCGGAGGCGAAGAGGGTGGGGGAGGCGGAGGCGTTCGCGCGGAGGGTGCTCGCGAGGCGCAGGAGGTTGGA[C/T]
TCGTAGGTGCTCCCCGCCGTGTAGTTGCCGCCGCTGGTGCCGCAGACAGGCCATGGCTGGGCGGCGGCGAGCGGGAGCGCGACCGCCGCGAAGAGGAGAA

Reverse complement sequence

TTCTCCTCTTCGCGGCGGTCGCGCTCCCGCTCGCCGCCGCCCAGCCATGGCCTGTCTGCGGCACCAGCGGCGGCAACTACACGGCGGGGAGCACCTACGA[G/A]
TCCAACCTCCTGCGCCTCGCGAGCACCCTCCGCGCGAACGCCTCCGCCTCCCCCACCCTCTTCGCCTCCGGCGTCCGCGGCGTCGGCCCGGACGCCGTCT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 50.00% 41.10% 0.99% 7.93% NA
All Indica  2759 76.50% 14.60% 1.12% 7.76% NA
All Japonica  1512 8.00% 81.20% 0.73% 10.05% NA
Aus  269 34.60% 61.70% 1.49% 2.23% NA
Indica I  595 83.00% 3.90% 1.18% 11.93% NA
Indica II  465 89.00% 9.00% 0.00% 1.94% NA
Indica III  913 64.80% 27.10% 1.64% 6.46% NA
Indica Intermediate  786 77.60% 11.70% 1.15% 9.54% NA
Temperate Japonica  767 8.20% 78.70% 0.65% 12.39% NA
Tropical Japonica  504 2.60% 89.90% 0.99% 6.55% NA
Japonica Intermediate  241 18.70% 71.00% 0.41% 9.96% NA
VI/Aromatic  96 6.20% 91.70% 0.00% 2.08% NA
Intermediate  90 35.60% 62.20% 1.11% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0721444659 C -> DEL LOC_Os07g35810.1 N frameshift_variant Average:88.95; most accessible tissue: Zhenshan97 young leaf, score: 98.668 N N N N
vg0721444659 C -> T LOC_Os07g35810.1 synonymous_variant ; p.Glu44Glu; LOW synonymous_codon Average:88.95; most accessible tissue: Zhenshan97 young leaf, score: 98.668 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)
vg0721444659 C T -0.04 -0.04 -0.02 -0.01 -0.02 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0721444659 NA 2.33E-07 mr1717 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
vg0721444659 NA 6.92E-07 mr1872 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
vg0721444659 NA 4.24E-07 mr1910 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
vg0721444659 NA 1.55E-10 mr1946 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
vg0721444659 NA 3.38E-13 mr1364_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
vg0721444659 NA 4.68E-08 mr1510_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
vg0721444659 NA 3.19E-18 mr1807_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
vg0721444659 NA 1.28E-06 mr1807_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