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Detailed information for vg0307302619:

Variant ID: vg0307302619 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 7302619
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AAATCCGTCTCGCGGTTTACTAACGGATACTGTAATTAGTTTTTTTATTAGTGTCCGAACACCCCATGCGATACCCTATATAATACCCGATATGACACGC[T/C]
AAAACTTTACACCACTGAATCTAAACACCCCATATTCATTTTTTGCAATGGCCCAATGGACTGCATGTCAGCACGGTTGAACCCCTGGCGCCCTTGTCTT

Reverse complement sequence

AAGACAAGGGCGCCAGGGGTTCAACCGTGCTGACATGCAGTCCATTGGGCCATTGCAAAAAATGAATATGGGGTGTTTAGATTCAGTGGTGTAAAGTTTT[A/G]
GCGTGTCATATCGGGTATTATATAGGGTATCGCATGGGGTGTTCGGACACTAATAAAAAAACTAATTACAGTATCCGTTAGTAAACCGCGAGACGGATTT

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 65.10% 32.90% 0.83% 1.14% NA
All Indica  2759 94.10% 3.00% 1.23% 1.74% NA
All Japonica  1512 4.80% 94.60% 0.20% 0.33% NA
Aus  269 98.50% 1.50% 0.00% 0.00% NA
Indica I  595 94.60% 0.00% 3.36% 2.02% NA
Indica II  465 96.60% 2.60% 0.22% 0.65% NA
Indica III  913 93.20% 5.50% 0.44% 0.88% NA
Indica Intermediate  786 93.10% 2.50% 1.15% 3.18% NA
Temperate Japonica  767 1.70% 97.30% 0.39% 0.65% NA
Tropical Japonica  504 10.70% 89.30% 0.00% 0.00% NA
Japonica Intermediate  241 2.50% 97.50% 0.00% 0.00% NA
VI/Aromatic  96 93.80% 6.20% 0.00% 0.00% NA
Intermediate  90 58.90% 37.80% 2.22% 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
vg0307302619 T -> C LOC_Os03g13500.1 upstream_gene_variant ; 3902.0bp to feature; MODIFIER silent_mutation Average:76.552; most accessible tissue: Minghui63 panicle, score: 91.586 N N N N
vg0307302619 T -> C LOC_Os03g13510.1 upstream_gene_variant ; 558.0bp to feature; MODIFIER silent_mutation Average:76.552; most accessible tissue: Minghui63 panicle, score: 91.586 N N N N
vg0307302619 T -> C LOC_Os03g13520.1 downstream_gene_variant ; 2636.0bp to feature; MODIFIER silent_mutation Average:76.552; most accessible tissue: Minghui63 panicle, score: 91.586 N N N N
vg0307302619 T -> C LOC_Os03g13510-LOC_Os03g13520 intergenic_region ; MODIFIER silent_mutation Average:76.552; most accessible tissue: Minghui63 panicle, score: 91.586 N N N N
vg0307302619 T -> DEL N N silent_mutation Average:76.552; most accessible tissue: Minghui63 panicle, score: 91.586 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)
vg0307302619 T C 0.02 0.01 0.0 0.0 0.01 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0307302619 NA 1.16E-90 mr1071 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
vg0307302619 NA 1.80E-90 mr1140 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
vg0307302619 NA 2.19E-27 mr1298 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
vg0307302619 NA 1.12E-22 mr1383 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
vg0307302619 NA 3.80E-35 mr1402 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
vg0307302619 NA 2.53E-76 mr1613 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
vg0307302619 NA 2.61E-92 mr1618 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
vg0307302619 NA 6.93E-53 mr1935 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
vg0307302619 NA 6.91E-09 mr1986 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
vg0307302619 NA 4.32E-108 mr1071_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
vg0307302619 NA 5.25E-102 mr1080_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
vg0307302619 NA 6.77E-114 mr1203_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
vg0307302619 NA 6.16E-13 mr1216_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
vg0307302619 NA 6.45E-22 mr1276_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
vg0307302619 NA 6.17E-15 mr1324_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
vg0307302619 NA 8.27E-07 mr1369_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
vg0307302619 NA 7.96E-20 mr1383_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
vg0307302619 NA 4.44E-07 mr1453_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
vg0307302619 2.59E-07 NA mr1499_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
vg0307302619 NA 6.82E-27 mr1617_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
vg0307302619 NA 1.18E-98 mr1619_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
vg0307302619 NA 1.58E-21 mr1682_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
vg0307302619 NA 8.03E-61 mr1695_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
vg0307302619 NA 4.97E-09 mr1705_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
vg0307302619 NA 4.46E-18 mr1817_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
vg0307302619 NA 1.33E-22 mr1968_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
vg0307302619 NA 1.43E-54 mr1991_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