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Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0821091267:

Variant ID: vg0821091267 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 21091267
Reference Allele: CAlternative Allele: T,A
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATCGGCGGCGCTATCGCCGTCGTGGTCGGCTGGTTGGCGCTCCGACGAGGATGACCGGTCGTTCAGGCTGCCGCTGCCTCCGCCGCCTCCATTGCCGCCG[C/T,A]
GGCTCACCGCCTGCCGGTACTTCTGCAGCAGCGGCAGAGAGCTTAACACTGTCAGAAACCAAGAACCGATGCAGACAGAGTTTGCGAGAAGCTGATCGGC

Reverse complement sequence

GCCGATCAGCTTCTCGCAAACTCTGTCTGCATCGGTTCTTGGTTTCTGACAGTGTTAAGCTCTCTGCCGCTGCTGCAGAAGTACCGGCAGGCGGTGAGCC[G/A,T]
CGGCGGCAATGGAGGCGGCGGAGGCAGCGGCAGCCTGAACGACCGGTCATCCTCGTCGGAGCGCCAACCAGCCGACCACGACGGCGATAGCGCCGCCGAT

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 94.30% 4.70% 0.95% 0.00% A: 0.02%
All Indica  2759 99.90% 0.10% 0.00% 0.00% NA
All Japonica  1512 85.90% 11.10% 2.98% 0.00% NA
Aus  269 99.60% 0.00% 0.00% 0.00% A: 0.37%
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 99.70% 0.30% 0.00% 0.00% NA
Temperate Japonica  767 86.70% 8.60% 4.69% 0.00% NA
Tropical Japonica  504 94.80% 4.60% 0.60% 0.00% NA
Japonica Intermediate  241 64.70% 32.80% 2.49% 0.00% NA
VI/Aromatic  96 51.00% 49.00% 0.00% 0.00% NA
Intermediate  90 95.60% 4.40% 0.00% 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
vg0821091267 C -> T LOC_Os08g33750.1 missense_variant ; p.Arg78His; MODERATE nonsynonymous_codon ; R78H Average:81.693; most accessible tissue: Zhenshan97 panicle, score: 88.062 unknown unknown DELETERIOUS 0.02
vg0821091267 C -> T LOC_Os08g33750.2 missense_variant ; p.Arg42His; MODERATE nonsynonymous_codon ; R42H Average:81.693; most accessible tissue: Zhenshan97 panicle, score: 88.062 unknown unknown DELETERIOUS 0.02
vg0821091267 C -> A LOC_Os08g33750.1 missense_variant ; p.Arg78Leu; MODERATE nonsynonymous_codon ; R78L Average:81.693; most accessible tissue: Zhenshan97 panicle, score: 88.062 unknown unknown TOLERATED 0.19
vg0821091267 C -> A LOC_Os08g33750.2 missense_variant ; p.Arg42Leu; MODERATE nonsynonymous_codon ; R42L Average:81.693; most accessible tissue: Zhenshan97 panicle, score: 88.062 unknown unknown TOLERATED 0.16

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)
vg0821091267 C A 0.0 0.0 0.0 -0.01 -0.01 0.0
vg0821091267 C T -0.01 -0.01 -0.01 0.0 -0.01 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0821091267 NA 6.71E-06 mr1807 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
vg0821091267 2.92E-07 3.16E-09 mr1531_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