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Detailed information for vg0619157347:

Variant ID: vg0619157347 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 19157347
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATTGGCAGGGTTGACGCCACGGTTCTTGAGCTCGCGGTACATCTGGCTGAGGGAACATCTGTCACAGAAGAGCTGCAGACAGCAGTCGGCGCAGGGCTCC[G/A]
GCGCCATGCCGAACGTGGCGCGGAGCTTCTGGCGGTAGGACCAAGAGTACATGGTGTGCATGCCTGGGAGCACCGTGCTCGGCCGCATCCAGCAGTAGGT

Reverse complement sequence

ACCTACTGCTGGATGCGGCCGAGCACGGTGCTCCCAGGCATGCACACCATGTACTCTTGGTCCTACCGCCAGAAGCTCCGCGCCACGTTCGGCATGGCGC[C/T]
GGAGCCCTGCGCCGACTGCTGTCTGCAGCTCTTCTGTGACAGATGTTCCCTCAGCCAGATGTACCGCGAGCTCAAGAACCGTGGCGTCAACCCTGCCAAT

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 56.20% 42.10% 0.40% 1.27% NA
All Indica  2759 88.40% 11.20% 0.40% 0.04% NA
All Japonica  1512 3.90% 92.30% 0.26% 3.57% NA
Aus  269 42.80% 57.20% 0.00% 0.00% NA
Indica I  595 92.90% 6.10% 0.84% 0.17% NA
Indica II  465 94.40% 5.40% 0.22% 0.00% NA
Indica III  913 91.30% 8.30% 0.33% 0.00% NA
Indica Intermediate  786 78.00% 21.80% 0.25% 0.00% NA
Temperate Japonica  767 5.00% 91.00% 0.26% 3.78% NA
Tropical Japonica  504 2.00% 96.60% 0.00% 1.39% NA
Japonica Intermediate  241 4.60% 87.10% 0.83% 7.47% NA
VI/Aromatic  96 3.10% 92.70% 0.00% 4.17% NA
Intermediate  90 45.60% 48.90% 4.44% 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
vg0619157347 G -> A LOC_Os06g32910.1 missense_variant ; p.Pro91Leu; MODERATE nonsynonymous_codon ; P91L Average:85.899; most accessible tissue: Zhenshan97 panicle, score: 96.043 unknown unknown DELETERIOUS 0.02
vg0619157347 G -> DEL LOC_Os06g32910.1 N frameshift_variant Average:85.899; most accessible tissue: Zhenshan97 panicle, score: 96.043 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)
vg0619157347 G A 0.05 0.0 -0.01 0.16 0.09 0.06

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0619157347 NA 5.28E-08 mr1043_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
vg0619157347 NA 1.68E-07 mr1111_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
vg0619157347 NA 1.72E-07 mr1167_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
vg0619157347 NA 6.33E-07 mr1185_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
vg0619157347 NA 6.50E-06 mr1263_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
vg0619157347 2.07E-06 3.92E-09 mr1269_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
vg0619157347 NA 6.09E-07 mr1291_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
vg0619157347 NA 6.22E-06 mr1458_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
vg0619157347 5.26E-06 2.11E-08 mr1479_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
vg0619157347 5.32E-06 8.42E-08 mr1677_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
vg0619157347 NA 1.68E-11 mr1680_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
vg0619157347 NA 1.21E-07 mr1680_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
vg0619157347 NA 1.24E-07 mr1726_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
vg0619157347 NA 5.88E-06 mr1736_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
vg0619157347 NA 3.77E-06 mr1740_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
vg0619157347 NA 4.58E-06 mr1829_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