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Detailed information for vg0222337580:

Variant ID: vg0222337580 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 22337580
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 313. )

Flanking Sequence (100 bp) in Reference Genome:


CGATGGTTCTTGATTCACCACACATTGTTGTCTACATTGCCAAAACGTATGCTTCAAGTGCCCAAAAGGCCGAAGCGGTCCGAGAAACATTATTCTGTCA[G/A]
GTATGTGTGATAAGCGGTTTCATATGCAACAATGCTGTAGGGACCCAAATGTTCACTGGCATCATGTACAGATACTTGTAGTACCAAAATTAGTTTAGCA

Reverse complement sequence

TGCTAAACTAATTTTGGTACTACAAGTATCTGTACATGATGCCAGTGAACATTTGGGTCCCTACAGCATTGTTGCATATGAAACCGCTTATCACACATAC[C/T]
TGACAGAATAATGTTTCTCGGACCGCTTCGGCCTTTTGGGCACTTGAAGCATACGTTTTGGCAATGTAGACAACAATGTGTGGTGAATCAAGAACCATCG

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 94.40% 5.00% 0.63% 0.00% NA
All Indica  2759 97.30% 2.30% 0.40% 0.00% NA
All Japonica  1512 89.60% 9.20% 1.26% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 90.10% 8.60% 1.34% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 99.80% 0.20% 0.00% 0.00% NA
Indica Intermediate  786 98.30% 1.30% 0.38% 0.00% NA
Temperate Japonica  767 94.30% 4.30% 1.43% 0.00% NA
Tropical Japonica  504 93.10% 6.50% 0.40% 0.00% NA
Japonica Intermediate  241 67.20% 30.30% 2.49% 0.00% NA
VI/Aromatic  96 72.90% 27.10% 0.00% 0.00% NA
Intermediate  90 94.40% 5.60% 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
vg0222337580 G -> A LOC_Os02g36974.1 3_prime_UTR_variant ; 447.0bp to feature; MODIFIER silent_mutation Average:91.879; most accessible tissue: Zhenshan97 young leaf, score: 94.848 N N N N
vg0222337580 G -> A LOC_Os02g36974.2 3_prime_UTR_variant ; 447.0bp to feature; MODIFIER silent_mutation Average:91.879; most accessible tissue: Zhenshan97 young leaf, score: 94.848 N N N N
vg0222337580 G -> A LOC_Os02g36974.6 3_prime_UTR_variant ; 447.0bp to feature; MODIFIER silent_mutation Average:91.879; most accessible tissue: Zhenshan97 young leaf, score: 94.848 N N N N
vg0222337580 G -> A LOC_Os02g36974.3 3_prime_UTR_variant ; 447.0bp to feature; MODIFIER silent_mutation Average:91.879; most accessible tissue: Zhenshan97 young leaf, score: 94.848 N N N N
vg0222337580 G -> A LOC_Os02g36974.4 3_prime_UTR_variant ; 447.0bp to feature; MODIFIER silent_mutation Average:91.879; most accessible tissue: Zhenshan97 young leaf, score: 94.848 N N N N
vg0222337580 G -> A LOC_Os02g36990.1 downstream_gene_variant ; 1958.0bp to feature; MODIFIER silent_mutation Average:91.879; most accessible tissue: Zhenshan97 young leaf, score: 94.848 N N N N
vg0222337580 G -> A LOC_Os02g36974.5 downstream_gene_variant ; 940.0bp to feature; MODIFIER silent_mutation Average:91.879; most accessible tissue: Zhenshan97 young leaf, score: 94.848 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)
vg0222337580 G A -0.04 -0.03 -0.02 -0.04 -0.07 -0.11

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0222337580 NA 3.71E-07 mr1098_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
vg0222337580 5.23E-06 5.23E-06 mr1186_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
vg0222337580 3.39E-07 3.39E-07 mr1192_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
vg0222337580 6.29E-08 6.29E-08 mr1245_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
vg0222337580 NA 1.51E-06 mr1267_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
vg0222337580 5.08E-06 5.08E-06 mr1311_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
vg0222337580 9.68E-06 9.68E-06 mr1312_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
vg0222337580 3.02E-08 3.02E-08 mr1329_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
vg0222337580 3.73E-06 3.73E-06 mr1337_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
vg0222337580 1.07E-06 1.07E-06 mr1373_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
vg0222337580 3.60E-06 3.60E-06 mr1442_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
vg0222337580 2.71E-06 2.71E-06 mr1445_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
vg0222337580 6.17E-06 6.17E-06 mr1524_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
vg0222337580 4.21E-06 4.21E-06 mr1616_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
vg0222337580 1.27E-07 1.27E-07 mr1645_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
vg0222337580 4.81E-08 4.81E-08 mr1647_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
vg0222337580 1.23E-07 1.23E-07 mr1648_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
vg0222337580 1.06E-07 1.06E-07 mr1652_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
vg0222337580 7.88E-07 7.88E-07 mr1655_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
vg0222337580 2.06E-06 2.06E-06 mr1663_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
vg0222337580 2.59E-06 2.59E-06 mr1669_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
vg0222337580 3.13E-06 3.13E-06 mr1674_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
vg0222337580 2.67E-07 2.66E-07 mr1688_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
vg0222337580 8.13E-09 8.13E-09 mr1697_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
vg0222337580 9.57E-06 9.57E-06 mr1832_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
vg0222337580 NA 6.48E-07 mr1833_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
vg0222337580 1.62E-06 1.62E-06 mr1843_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
vg0222337580 9.50E-06 9.50E-06 mr1847_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
vg0222337580 NA 5.78E-07 mr1851_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
vg0222337580 NA 2.35E-06 mr1861_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