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Detailed information for vg1004262486:

Variant ID: vg1004262486 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 4262486
Reference Allele: TAlternative Allele: A,C
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.75, A: 0.24, C: 0.01, others allele: 0.00, population size: 99. )

Flanking Sequence (100 bp) in Reference Genome:


GAAAAATCCAGTCGCCTTGGCAATTTAGCATCCCTAAATTTCAATAAAATTTAATGTTTTATCGGCGAAAAAATCATGCAGCCCTTTCGAAATCTCCTCC[T/A,C]
CTTTGCGAGTAAAAAAACCCTCGGCTACGGGCTATCCACAAACTGCCATCGACGGATACTGTGTGGGTCGCCCATGGCGATTGGCCACAGCCGCTGCCGC

Reverse complement sequence

GCGGCAGCGGCTGTGGCCAATCGCCATGGGCGACCCACACAGTATCCGTCGATGGCAGTTTGTGGATAGCCCGTAGCCGAGGGTTTTTTTACTCGCAAAG[A/T,G]
GGAGGAGATTTCGAAAGGGCTGCATGATTTTTTCGCCGATAAAACATTAAATTTTATTGAAATTTAGGGATGCTAAATTGCCAAGGCGACTGGATTTTTC

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 68.80% 31.00% 0.11% 0.00% C: 0.13%
All Indica  2759 78.50% 21.20% 0.18% 0.00% C: 0.07%
All Japonica  1512 65.30% 34.70% 0.00% 0.00% C: 0.07%
Aus  269 4.80% 95.20% 0.00% 0.00% NA
Indica I  595 58.50% 41.30% 0.17% 0.00% NA
Indica II  465 83.90% 15.50% 0.65% 0.00% NA
Indica III  913 87.80% 12.20% 0.00% 0.00% NA
Indica Intermediate  786 79.60% 20.00% 0.13% 0.00% C: 0.25%
Temperate Japonica  767 94.10% 5.90% 0.00% 0.00% NA
Tropical Japonica  504 17.50% 82.50% 0.00% 0.00% NA
Japonica Intermediate  241 73.40% 26.10% 0.00% 0.00% C: 0.41%
VI/Aromatic  96 30.20% 66.70% 0.00% 0.00% C: 3.12%
Intermediate  90 62.20% 37.80% 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
vg1004262486 T -> C LOC_Os10g07974.1 upstream_gene_variant ; 2082.0bp to feature; MODIFIER silent_mutation Average:83.539; most accessible tissue: Zhenshan97 flag leaf, score: 91.729 N N N N
vg1004262486 T -> C LOC_Os10g07978.1 upstream_gene_variant ; 29.0bp to feature; MODIFIER silent_mutation Average:83.539; most accessible tissue: Zhenshan97 flag leaf, score: 91.729 N N N N
vg1004262486 T -> C LOC_Os10g07978.2 upstream_gene_variant ; 29.0bp to feature; MODIFIER silent_mutation Average:83.539; most accessible tissue: Zhenshan97 flag leaf, score: 91.729 N N N N
vg1004262486 T -> C LOC_Os10g07974-LOC_Os10g07978 intergenic_region ; MODIFIER silent_mutation Average:83.539; most accessible tissue: Zhenshan97 flag leaf, score: 91.729 N N N N
vg1004262486 T -> A LOC_Os10g07974.1 upstream_gene_variant ; 2082.0bp to feature; MODIFIER silent_mutation Average:83.539; most accessible tissue: Zhenshan97 flag leaf, score: 91.729 N N N N
vg1004262486 T -> A LOC_Os10g07978.1 upstream_gene_variant ; 29.0bp to feature; MODIFIER silent_mutation Average:83.539; most accessible tissue: Zhenshan97 flag leaf, score: 91.729 N N N N
vg1004262486 T -> A LOC_Os10g07978.2 upstream_gene_variant ; 29.0bp to feature; MODIFIER silent_mutation Average:83.539; most accessible tissue: Zhenshan97 flag leaf, score: 91.729 N N N N
vg1004262486 T -> A LOC_Os10g07974-LOC_Os10g07978 intergenic_region ; MODIFIER silent_mutation Average:83.539; most accessible tissue: Zhenshan97 flag leaf, score: 91.729 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)
vg1004262486 T A 0.02 0.03 0.0 0.02 0.01 0.02
vg1004262486 T C 0.04 0.03 -0.03 0.04 0.02 0.03

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1004262486 NA 1.23E-12 Grain_width 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
vg1004262486 NA 7.21E-08 mr1308 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
vg1004262486 NA 3.23E-07 mr1471 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
vg1004262486 NA 1.80E-07 mr1584 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
vg1004262486 NA 1.94E-06 mr1642 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
vg1004262486 NA 4.00E-06 mr1830 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
vg1004262486 5.98E-07 NA mr1853 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
vg1004262486 2.67E-06 2.67E-06 mr1853 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
vg1004262486 NA 1.33E-07 mr1870 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
vg1004262486 NA 4.39E-10 mr1942 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
vg1004262486 NA 1.77E-09 mr1019_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
vg1004262486 NA 6.08E-08 mr1261_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
vg1004262486 NA 2.05E-08 mr1304_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
vg1004262486 NA 5.61E-07 mr1308_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
vg1004262486 NA 6.58E-06 mr1398_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
vg1004262486 NA 3.83E-08 mr1401_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
vg1004262486 NA 9.30E-10 mr1584_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
vg1004262486 NA 2.35E-06 mr1606_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
vg1004262486 NA 3.04E-09 mr1642_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
vg1004262486 NA 7.84E-07 mr1653_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
vg1004262486 NA 3.02E-08 mr1696_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
vg1004262486 NA 6.60E-06 mr1707_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
vg1004262486 NA 2.19E-08 mr1817_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
vg1004262486 NA 3.20E-06 mr1853_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
vg1004262486 NA 3.10E-12 mr1942_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
vg1004262486 NA 6.08E-09 mr1942_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