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Detailed information for vg1101631388:

Variant ID: vg1101631388 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 1631388
Reference Allele: TAlternative Allele: G
Primary Allele: TSecondary Allele: G

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.91, G: 0.09, others allele: 0.00, population size: 111. )

Flanking Sequence (100 bp) in Reference Genome:


TAGGAATAGGATGGCCAAGACAGAGTCAGAGAAGGACTTGTGAAGCAGGCAGAGGCAGGAGAAGGCCACCGCAGGCAGGACGAGGTAGGAGATGATGTGG[T/G]
GGAGATTGACAAAGGCAAACAACGGTGGCGAGAGGGGAGAGGAGTCGAGTGGGTCAAGCCATATAAATGGATGGCTGCTGGTGGTTTTGTCTCTTGGTAC

Reverse complement sequence

GTACCAAGAGACAAAACCACCAGCAGCCATCCATTTATATGGCTTGACCCACTCGACTCCTCTCCCCTCTCGCCACCGTTGTTTGCCTTTGTCAATCTCC[A/C]
CCACATCATCTCCTACCTCGTCCTGCCTGCGGTGGCCTTCTCCTGCCTCTGCCTGCTTCACAAGTCCTTCTCTGACTCTGTCTTGGCCATCCTATTCCTA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 51.60% 47.90% 0.23% 0.30% NA
All Indica  2759 26.60% 72.60% 0.40% 0.40% NA
All Japonica  1512 96.60% 3.40% 0.00% 0.00% NA
Aus  269 52.00% 47.20% 0.00% 0.74% NA
Indica I  595 81.80% 17.00% 0.67% 0.50% NA
Indica II  465 11.60% 88.00% 0.00% 0.43% NA
Indica III  913 0.80% 99.20% 0.00% 0.00% NA
Indica Intermediate  786 23.70% 74.70% 0.89% 0.76% NA
Temperate Japonica  767 97.90% 2.10% 0.00% 0.00% NA
Tropical Japonica  504 95.60% 4.40% 0.00% 0.00% NA
Japonica Intermediate  241 94.60% 5.40% 0.00% 0.00% NA
VI/Aromatic  96 51.00% 49.00% 0.00% 0.00% NA
Intermediate  90 58.90% 40.00% 0.00% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1101631388 T -> DEL N N silent_mutation Average:79.873; most accessible tissue: Callus, score: 94.037 N N N N
vg1101631388 T -> G LOC_Os11g04030.1 5_prime_UTR_variant ; 162.0bp to feature; MODIFIER silent_mutation Average:79.873; most accessible tissue: Callus, score: 94.037 N N N N
vg1101631388 T -> G LOC_Os11g04030.4 5_prime_UTR_variant ; 1853.0bp to feature; MODIFIER silent_mutation Average:79.873; most accessible tissue: Callus, score: 94.037 N N N N
vg1101631388 T -> G LOC_Os11g04030.2 5_prime_UTR_variant ; 162.0bp to feature; MODIFIER silent_mutation Average:79.873; most accessible tissue: Callus, score: 94.037 N N N N
vg1101631388 T -> G LOC_Os11g04040.1 upstream_gene_variant ; 3263.0bp to feature; MODIFIER silent_mutation Average:79.873; most accessible tissue: Callus, score: 94.037 N N N N
vg1101631388 T -> G LOC_Os11g04030.3 upstream_gene_variant ; 1135.0bp to feature; MODIFIER silent_mutation Average:79.873; most accessible tissue: Callus, score: 94.037 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)
vg1101631388 T G -0.09 -0.06 -0.03 0.0 -0.03 -0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1101631388 NA 1.24E-09 mr1904 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
vg1101631388 NA 1.64E-07 mr1041_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
vg1101631388 NA 1.26E-07 mr1170_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
vg1101631388 NA 8.53E-09 mr1184_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
vg1101631388 NA 7.97E-08 mr1278_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
vg1101631388 NA 1.78E-06 mr1293_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
vg1101631388 NA 3.65E-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
vg1101631388 NA 5.51E-06 mr1329_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
vg1101631388 NA 2.19E-06 mr1374_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
vg1101631388 NA 1.62E-08 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
vg1101631388 NA 4.37E-07 mr1419_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
vg1101631388 NA 2.00E-07 mr1420_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
vg1101631388 NA 3.11E-06 mr1467_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
vg1101631388 NA 4.70E-08 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
vg1101631388 NA 9.17E-06 mr1492_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
vg1101631388 NA 7.23E-10 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
vg1101631388 NA 9.81E-07 mr1508_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
vg1101631388 NA 3.83E-07 mr1524_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
vg1101631388 NA 1.34E-07 mr1556_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
vg1101631388 NA 3.47E-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
vg1101631388 NA 5.82E-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
vg1101631388 NA 2.87E-10 mr1659_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
vg1101631388 8.76E-06 8.66E-12 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
vg1101631388 NA 5.66E-06 mr1687_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
vg1101631388 NA 2.21E-06 mr1764_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
vg1101631388 NA 2.01E-06 mr1779_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
vg1101631388 NA 6.16E-07 mr1812_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
vg1101631388 NA 7.44E-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
vg1101631388 NA 6.56E-17 mr1838_2 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
vg1101631388 NA 3.78E-06 mr1838_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
vg1101631388 NA 4.75E-06 mr1843_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
vg1101631388 NA 1.65E-06 mr1992_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