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Detailed information for vg0722679489:

Variant ID: vg0722679489 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 22679489
Reference Allele: CAlternative Allele: T,A
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.65, T: 0.35, others allele: 0.00, population size: 84. )

Flanking Sequence (100 bp) in Reference Genome:


ATTAACTCATGATTAATTGAGTATTAACTATTTTAAATTTCAAAAATGGATTATTATGATTTTTTAAAGCAACTTTCCTATAGAAATTTTTTGCAAAAAA[C/T,A]
GTACCGTTTAGTAGTTTAAAAAGCGTGCACGCGGAAAACGAGAATCAATCTCCCCTATTATCTCCTCAGAACGAACAGAGCCTAAAGGCCGAAGCTTTTC

Reverse complement sequence

GAAAAGCTTCGGCCTTTAGGCTCTGTTCGTTCTGAGGAGATAATAGGGGAGATTGATTCTCGTTTTCCGCGTGCACGCTTTTTAAACTACTAAACGGTAC[G/A,T]
TTTTTTGCAAAAAATTTCTATAGGAAAGTTGCTTTAAAAAATCATAATAATCCATTTTTGAAATTTAAAATAGTTAATACTCAATTAATCATGAGTTAAT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 55.80% 42.90% 0.78% 0.36% A: 0.08%
All Indica  2759 79.70% 19.80% 0.47% 0.04% NA
All Japonica  1512 17.70% 81.50% 0.60% 0.00% A: 0.26%
Aus  269 24.90% 75.10% 0.00% 0.00% NA
Indica I  595 99.20% 0.70% 0.17% 0.00% NA
Indica II  465 66.90% 32.70% 0.43% 0.00% NA
Indica III  913 75.00% 24.40% 0.55% 0.00% NA
Indica Intermediate  786 77.90% 21.40% 0.64% 0.13% NA
Temperate Japonica  767 2.60% 95.70% 1.17% 0.00% A: 0.52%
Tropical Japonica  504 42.70% 57.30% 0.00% 0.00% NA
Japonica Intermediate  241 13.30% 86.70% 0.00% 0.00% NA
VI/Aromatic  96 66.70% 5.20% 11.46% 16.67% NA
Intermediate  90 47.80% 47.80% 4.44% 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
vg0722679489 C -> DEL N N silent_mutation Average:80.249; most accessible tissue: Callus, score: 95.593 N N N N
vg0722679489 C -> A LOC_Os07g37810.1 upstream_gene_variant ; 2740.0bp to feature; MODIFIER silent_mutation Average:80.249; most accessible tissue: Callus, score: 95.593 N N N N
vg0722679489 C -> A LOC_Os07g37810.2 upstream_gene_variant ; 2740.0bp to feature; MODIFIER silent_mutation Average:80.249; most accessible tissue: Callus, score: 95.593 N N N N
vg0722679489 C -> A LOC_Os07g37820.1 downstream_gene_variant ; 1467.0bp to feature; MODIFIER silent_mutation Average:80.249; most accessible tissue: Callus, score: 95.593 N N N N
vg0722679489 C -> A LOC_Os07g37810-LOC_Os07g37820 intergenic_region ; MODIFIER silent_mutation Average:80.249; most accessible tissue: Callus, score: 95.593 N N N N
vg0722679489 C -> T LOC_Os07g37810.1 upstream_gene_variant ; 2740.0bp to feature; MODIFIER silent_mutation Average:80.249; most accessible tissue: Callus, score: 95.593 N N N N
vg0722679489 C -> T LOC_Os07g37810.2 upstream_gene_variant ; 2740.0bp to feature; MODIFIER silent_mutation Average:80.249; most accessible tissue: Callus, score: 95.593 N N N N
vg0722679489 C -> T LOC_Os07g37820.1 downstream_gene_variant ; 1467.0bp to feature; MODIFIER silent_mutation Average:80.249; most accessible tissue: Callus, score: 95.593 N N N N
vg0722679489 C -> T LOC_Os07g37810-LOC_Os07g37820 intergenic_region ; MODIFIER silent_mutation Average:80.249; most accessible tissue: Callus, score: 95.593 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)
vg0722679489 C A 0.01 -0.01 -0.02 0.0 -0.01 -0.01
vg0722679489 C T -0.03 -0.03 -0.03 -0.03 -0.04 -0.04

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0722679489 NA 9.35E-06 mr1124 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
vg0722679489 NA 3.63E-06 mr1170 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
vg0722679489 NA 9.69E-07 mr1622 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
vg0722679489 NA 1.43E-06 mr1679 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
vg0722679489 NA 4.96E-07 mr1717 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
vg0722679489 NA 4.22E-06 mr1720 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
vg0722679489 NA 1.39E-06 mr1168_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
vg0722679489 NA 1.94E-06 mr1170_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
vg0722679489 NA 4.56E-06 mr1188_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
vg0722679489 NA 8.88E-06 mr1252_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
vg0722679489 8.12E-06 8.11E-06 mr1356_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
vg0722679489 9.21E-06 9.21E-06 mr1405_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
vg0722679489 NA 8.04E-08 mr1607_2 Ind_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
vg0722679489 NA 8.33E-10 mr1679_2 Ind_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
vg0722679489 NA 1.51E-08 mr1691_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
vg0722679489 NA 3.61E-06 mr1711_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
vg0722679489 NA 2.42E-07 mr1720_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
vg0722679489 NA 1.36E-06 mr1798_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
vg0722679489 NA 4.51E-07 mr1830_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
vg0722679489 NA 2.82E-06 mr1835_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