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Detailed information for vg0725046371:

Variant ID: vg0725046371 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 25046371
Reference Allele: AAlternative Allele: C
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 295. )

Flanking Sequence (100 bp) in Reference Genome:


TTGGCAATGGCAATTGATTTTGGAATGAATAAGAATTGTACCTGACTACCTGAACTAGGAATTAGGATGGCCGCTCTTGCTTGGATCGTCGTGTACCAAG[A/C]
AAGAGCTTGCTGCCTTCAGTGTTCATCTTTCTCTTGTCGCGCTGCCTACAAATGTGCATGTCAGATAGTCTTGTTAACCACAACTCGGTGCTATGCCTCT

Reverse complement sequence

AGAGGCATAGCACCGAGTTGTGGTTAACAAGACTATCTGACATGCACATTTGTAGGCAGCGCGACAAGAGAAAGATGAACACTGAAGGCAGCAAGCTCTT[T/G]
CTTGGTACACGACGATCCAAGCAAGAGCGGCCATCCTAATTCCTAGTTCAGGTAGTCAGGTACAATTCTTATTCATTCCAAAATCAATTGCCATTGCCAA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 64.30% 35.30% 0.04% 0.30% NA
All Indica  2759 96.30% 3.30% 0.07% 0.40% NA
All Japonica  1512 2.80% 97.10% 0.00% 0.07% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 98.00% 1.30% 0.17% 0.50% NA
Indica II  465 90.50% 8.80% 0.00% 0.65% NA
Indica III  913 99.20% 0.40% 0.00% 0.33% NA
Indica Intermediate  786 94.90% 4.70% 0.13% 0.25% NA
Temperate Japonica  767 4.60% 95.40% 0.00% 0.00% NA
Tropical Japonica  504 0.00% 100.00% 0.00% 0.00% NA
Japonica Intermediate  241 3.30% 96.30% 0.00% 0.41% NA
VI/Aromatic  96 32.30% 67.70% 0.00% 0.00% NA
Intermediate  90 46.70% 51.10% 0.00% 2.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0725046371 A -> DEL N N silent_mutation Average:79.409; most accessible tissue: Zhenshan97 flower, score: 90.95 N N N N
vg0725046371 A -> C LOC_Os07g41810.2 3_prime_UTR_variant ; 203.0bp to feature; MODIFIER silent_mutation Average:79.409; most accessible tissue: Zhenshan97 flower, score: 90.95 N N N N
vg0725046371 A -> C LOC_Os07g41820.1 upstream_gene_variant ; 2745.0bp to feature; MODIFIER silent_mutation Average:79.409; most accessible tissue: Zhenshan97 flower, score: 90.95 N N N N
vg0725046371 A -> C LOC_Os07g41800.1 downstream_gene_variant ; 2636.0bp to feature; MODIFIER silent_mutation Average:79.409; most accessible tissue: Zhenshan97 flower, score: 90.95 N N N N
vg0725046371 A -> C LOC_Os07g41800.2 downstream_gene_variant ; 2636.0bp to feature; MODIFIER silent_mutation Average:79.409; most accessible tissue: Zhenshan97 flower, score: 90.95 N N N N
vg0725046371 A -> C LOC_Os07g41800.3 downstream_gene_variant ; 2636.0bp to feature; MODIFIER silent_mutation Average:79.409; most accessible tissue: Zhenshan97 flower, score: 90.95 N N N N
vg0725046371 A -> C LOC_Os07g41810.1 intron_variant ; MODIFIER silent_mutation Average:79.409; most accessible tissue: Zhenshan97 flower, score: 90.95 N N N N
vg0725046371 A -> C LOC_Os07g41810.3 intron_variant ; MODIFIER silent_mutation Average:79.409; most accessible tissue: Zhenshan97 flower, score: 90.95 N N N N
vg0725046371 A -> C LOC_Os07g41810.4 intron_variant ; MODIFIER silent_mutation Average:79.409; most accessible tissue: Zhenshan97 flower, score: 90.95 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)
vg0725046371 A C -0.01 0.01 0.0 0.0 -0.02 -0.05

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0725046371 NA 2.27E-09 Awn_length Jap_All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0725046371 NA 6.07E-21 mr1021 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
vg0725046371 NA 4.07E-10 mr1050 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
vg0725046371 NA 1.07E-06 mr1245 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
vg0725046371 NA 2.56E-12 mr1272 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
vg0725046371 NA 1.00E-16 mr1276 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
vg0725046371 8.34E-06 1.87E-19 mr1324 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
vg0725046371 NA 4.96E-12 mr1325 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
vg0725046371 NA 5.81E-14 mr1326 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
vg0725046371 NA 3.03E-31 mr1333 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
vg0725046371 NA 6.93E-16 mr1335 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
vg0725046371 NA 1.54E-06 mr1354 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
vg0725046371 NA 1.26E-08 mr1488 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
vg0725046371 NA 2.09E-08 mr1506 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
vg0725046371 NA 1.08E-19 mr1580 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
vg0725046371 NA 9.48E-28 mr1686 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
vg0725046371 NA 3.07E-07 mr1690 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
vg0725046371 NA 4.89E-07 mr1797 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
vg0725046371 NA 4.89E-07 mr1801 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
vg0725046371 NA 2.98E-23 mr1817 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
vg0725046371 NA 8.63E-07 mr1886 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
vg0725046371 NA 4.37E-15 mr1924 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
vg0725046371 NA 5.91E-07 mr1979 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
vg0725046371 NA 1.83E-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
vg0725046371 NA 3.52E-09 mr1050_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
vg0725046371 9.97E-06 9.97E-06 mr1169_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
vg0725046371 NA 4.43E-18 mr1239_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
vg0725046371 NA 1.80E-06 mr1272_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
vg0725046371 NA 2.48E-14 mr1333_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
vg0725046371 NA 1.53E-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
vg0725046371 NA 8.62E-06 mr1549_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
vg0725046371 NA 2.69E-06 mr1574_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
vg0725046371 NA 2.17E-10 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
vg0725046371 NA 8.39E-09 mr1681_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
vg0725046371 NA 3.14E-16 mr1686_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
vg0725046371 NA 2.29E-06 mr1757_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