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Detailed information for vg1105604948:

Variant ID: vg1105604948 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 5604948
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.95, A: 0.05, others allele: 0.00, population size: 85. )

Flanking Sequence (100 bp) in Reference Genome:


CAATGCCCTGTTGGACCGAACTTCCAAGAAATTCTAAGAACCAACCGTATCAGTCCAACCACTGAGAGTAAGTATAATACTGAGCTATAAACCTACTATA[G/A]
CTTAGGTGGAGGAGAGAGATAGTAAATAAGAGCTAGCTTATCACAAACTCCAAAACAAATACATTAAATATATAAGTGAGAGATAAAGAGAATAGAAGAA

Reverse complement sequence

TTCTTCTATTCTCTTTATCTCTCACTTATATATTTAATGTATTTGTTTTGGAGTTTGTGATAAGCTAGCTCTTATTTACTATCTCTCTCCTCCACCTAAG[C/T]
TATAGTAGGTTTATAGCTCAGTATTATACTTACTCTCAGTGGTTGGACTGATACGGTTGGTTCTTAGAATTTCTTGGAAGTTCGGTCCAACAGGGCATTG

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 55.20% 34.90% 0.23% 9.67% NA
All Indica  2759 80.00% 14.10% 0.18% 5.73% NA
All Japonica  1512 6.00% 80.80% 0.07% 13.16% NA
Aus  269 92.60% 3.70% 0.37% 3.35% NA
Indica I  595 74.30% 12.40% 0.17% 13.11% NA
Indica II  465 94.00% 4.90% 0.22% 0.86% NA
Indica III  913 81.10% 13.70% 0.22% 5.04% NA
Indica Intermediate  786 74.90% 21.10% 0.13% 3.82% NA
Temperate Japonica  767 2.50% 88.70% 0.13% 8.74% NA
Tropical Japonica  504 10.30% 78.40% 0.00% 11.31% NA
Japonica Intermediate  241 8.30% 60.60% 0.00% 31.12% NA
VI/Aromatic  96 12.50% 0.00% 2.08% 85.42% NA
Intermediate  90 52.20% 35.60% 2.22% 10.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1105604948 G -> A LOC_Os11g10310.1 upstream_gene_variant ; 1871.0bp to feature; MODIFIER silent_mutation Average:83.382; most accessible tissue: Callus, score: 93.525 N N N N
vg1105604948 G -> A LOC_Os11g10320.1 upstream_gene_variant ; 295.0bp to feature; MODIFIER silent_mutation Average:83.382; most accessible tissue: Callus, score: 93.525 N N N N
vg1105604948 G -> A LOC_Os11g10310-LOC_Os11g10320 intergenic_region ; MODIFIER silent_mutation Average:83.382; most accessible tissue: Callus, score: 93.525 N N N N
vg1105604948 G -> DEL N N silent_mutation Average:83.382; most accessible tissue: Callus, score: 93.525 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)
vg1105604948 G A -0.05 -0.11 -0.1 -0.03 -0.03 -0.04

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1105604948 1.85E-06 NA mr1003 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
vg1105604948 5.08E-06 NA mr1051 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
vg1105604948 NA 9.87E-15 mr1653 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
vg1105604948 NA 1.19E-07 mr1205_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
vg1105604948 NA 8.06E-10 mr1232_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
vg1105604948 NA 3.35E-07 mr1275_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
vg1105604948 NA 8.72E-06 mr1289_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
vg1105604948 NA 9.19E-06 mr1294_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
vg1105604948 NA 8.86E-06 mr1294_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
vg1105604948 NA 1.84E-07 mr1302_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
vg1105604948 NA 7.68E-07 mr1418_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
vg1105604948 NA 8.72E-06 mr1428_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
vg1105604948 NA 2.46E-07 mr1488_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
vg1105604948 NA 1.02E-09 mr1506_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
vg1105604948 NA 8.11E-13 mr1521_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
vg1105604948 NA 2.96E-17 mr1557_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
vg1105604948 NA 6.46E-08 mr1604_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
vg1105604948 NA 9.21E-12 mr1641_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
vg1105604948 NA 7.07E-11 mr1646_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
vg1105604948 NA 1.42E-25 mr1653_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
vg1105604948 NA 1.45E-07 mr1653_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
vg1105604948 NA 3.36E-08 mr1683_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
vg1105604948 NA 4.85E-07 mr1723_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
vg1105604948 NA 1.45E-08 mr1824_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
vg1105604948 NA 5.82E-06 mr1876_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
vg1105604948 NA 2.04E-11 mr1986_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