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Detailed information for vg0137962179:

Variant ID: vg0137962179 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 37962179
Reference Allele: TAlternative Allele: A
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AATTAATACAAAGATAAAATAATAAGAATGTTTTCTACTTTGTTTATAGGGGTGAGGGTACGTTCGTGTGAGTGTCTACGTTGTACTGTGTAATTTTTTT[T/A]
AAAAATATACTATATTAAAATTACAATTGATCCCACTGTATCGAGTTTAATTTATCCTTCATTTTTACTAACTTTTTTTTCTTGTCATGTAACAAATTTT

Reverse complement sequence

AAAATTTGTTACATGACAAGAAAAAAAAGTTAGTAAAAATGAAGGATAAATTAAACTCGATACAGTGGGATCAATTGTAATTTTAATATAGTATATTTTT[A/T]
AAAAAAATTACACAGTACAACGTAGACACTCACACGAACGTACCCTCACCCCTATAAACAAAGTAGAAAACATTCTTATTATTTTATCTTTGTATTAATT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 67.30% 31.30% 1.44% 0.00% NA
All Indica  2759 98.20% 1.70% 0.07% 0.00% NA
All Japonica  1512 10.50% 85.10% 4.37% 0.00% NA
Aus  269 97.80% 2.20% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.40% 0.60% 0.00% 0.00% NA
Indica III  913 99.30% 0.50% 0.11% 0.00% NA
Indica Intermediate  786 94.90% 5.00% 0.13% 0.00% NA
Temperate Japonica  767 16.70% 74.80% 8.47% 0.00% NA
Tropical Japonica  504 3.40% 96.40% 0.20% 0.00% NA
Japonica Intermediate  241 5.80% 94.20% 0.00% 0.00% NA
VI/Aromatic  96 4.20% 95.80% 0.00% 0.00% NA
Intermediate  90 48.90% 51.10% 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
vg0137962179 T -> A LOC_Os01g65400.2 upstream_gene_variant ; 3178.0bp to feature; MODIFIER silent_mutation Average:98.874; most accessible tissue: Callus, score: 99.687 N N N N
vg0137962179 T -> A LOC_Os01g65410.1 upstream_gene_variant ; 363.0bp to feature; MODIFIER silent_mutation Average:98.874; most accessible tissue: Callus, score: 99.687 N N N N
vg0137962179 T -> A LOC_Os01g65400.4 upstream_gene_variant ; 3190.0bp to feature; MODIFIER silent_mutation Average:98.874; most accessible tissue: Callus, score: 99.687 N N N N
vg0137962179 T -> A LOC_Os01g65400.5 upstream_gene_variant ; 3190.0bp to feature; MODIFIER silent_mutation Average:98.874; most accessible tissue: Callus, score: 99.687 N N N N
vg0137962179 T -> A LOC_Os01g65400.3 upstream_gene_variant ; 3190.0bp to feature; MODIFIER silent_mutation Average:98.874; most accessible tissue: Callus, score: 99.687 N N N N
vg0137962179 T -> A LOC_Os01g65400.1 upstream_gene_variant ; 3190.0bp to feature; MODIFIER silent_mutation Average:98.874; most accessible tissue: Callus, score: 99.687 N N N N
vg0137962179 T -> A LOC_Os01g65400-LOC_Os01g65410 intergenic_region ; MODIFIER silent_mutation Average:98.874; most accessible tissue: Callus, score: 99.687 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)
vg0137962179 T A 0.0 0.0 0.0 0.0 0.0 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0137962179 NA 1.40E-19 Yield 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
vg0137962179 2.42E-09 NA mr1134 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
vg0137962179 6.66E-11 5.84E-78 mr1135 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
vg0137962179 NA 4.58E-25 mr1375 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
vg0137962179 1.96E-08 NA mr1504 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
vg0137962179 4.08E-06 4.53E-89 mr1517 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
vg0137962179 NA 1.30E-71 mr1538 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
vg0137962179 NA 1.49E-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
vg0137962179 3.93E-06 1.66E-37 mr1670 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
vg0137962179 1.46E-06 NA mr1672 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
vg0137962179 NA 5.35E-11 mr1751 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
vg0137962179 8.96E-08 NA mr1134_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
vg0137962179 NA 1.62E-09 mr1198_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
vg0137962179 NA 1.07E-12 mr1217_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
vg0137962179 2.48E-06 7.63E-07 mr1305_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
vg0137962179 1.58E-06 NA mr1379_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
vg0137962179 7.84E-06 NA mr1379_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
vg0137962179 4.19E-06 NA mr1504_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
vg0137962179 NA 2.22E-09 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
vg0137962179 7.96E-06 NA mr1517_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
vg0137962179 1.37E-06 NA mr1559_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
vg0137962179 5.59E-06 9.69E-06 mr1559_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
vg0137962179 5.75E-15 2.11E-60 mr1670_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
vg0137962179 2.47E-06 2.47E-06 mr1670_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