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Detailed information for vg0429867566:

Variant ID: vg0429867566 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 29867566
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.90, T: 0.10, others allele: 0.00, population size: 94. )

Flanking Sequence (100 bp) in Reference Genome:


ATATGTTGGGCCCACATGTCAGTGGGCCCCACCTTTTTTATGTGTGTGAATGACAAACGGATCCCACATATACGTTTTTAATTCAAATGACATCTAAGCG[T/C]
CATGTCAACCCACAGACATGTCAACACCGCCACGTCAGCGAAACCGCCCTCCAAAACCGCTAAGGAAGTCAAATTGCACCGATTTCAATAGTTCGGGGGA

Reverse complement sequence

TCCCCCGAACTATTGAAATCGGTGCAATTTGACTTCCTTAGCGGTTTTGGAGGGCGGTTTCGCTGACGTGGCGGTGTTGACATGTCTGTGGGTTGACATG[A/G]
CGCTTAGATGTCATTTGAATTAAAAACGTATATGTGGGATCCGTTTGTCATTCACACACATAAAAAAGGTGGGGCCCACTGACATGTGGGCCCAACATAT

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 57.30% 42.10% 0.47% 0.11% NA
All Indica  2759 56.60% 42.60% 0.58% 0.18% NA
All Japonica  1512 67.50% 32.30% 0.13% 0.00% NA
Aus  269 29.70% 70.30% 0.00% 0.00% NA
Indica I  595 78.20% 21.80% 0.00% 0.00% NA
Indica II  465 24.30% 74.80% 0.43% 0.43% NA
Indica III  913 57.90% 41.70% 0.22% 0.11% NA
Indica Intermediate  786 57.90% 40.30% 1.53% 0.25% NA
Temperate Japonica  767 52.20% 47.60% 0.26% 0.00% NA
Tropical Japonica  504 93.70% 6.30% 0.00% 0.00% NA
Japonica Intermediate  241 61.80% 38.20% 0.00% 0.00% NA
VI/Aromatic  96 2.10% 96.90% 1.04% 0.00% NA
Intermediate  90 50.00% 46.70% 3.33% 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
vg0429867566 T -> C LOC_Os04g50070.1 downstream_gene_variant ; 3730.0bp to feature; MODIFIER silent_mutation Average:92.897; most accessible tissue: Zhenshan97 panicle, score: 98.955 N N N N
vg0429867566 T -> C LOC_Os04g50080.1 downstream_gene_variant ; 412.0bp to feature; MODIFIER silent_mutation Average:92.897; most accessible tissue: Zhenshan97 panicle, score: 98.955 N N N N
vg0429867566 T -> C LOC_Os04g50080-LOC_Os04g50090 intergenic_region ; MODIFIER silent_mutation Average:92.897; most accessible tissue: Zhenshan97 panicle, score: 98.955 N N N N
vg0429867566 T -> DEL N N silent_mutation Average:92.897; most accessible tissue: Zhenshan97 panicle, score: 98.955 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)
vg0429867566 T C -0.03 -0.02 -0.01 -0.02 -0.02 -0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0429867566 NA 9.36E-11 mr1169 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
vg0429867566 1.06E-07 3.87E-16 mr1174 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
vg0429867566 NA 1.29E-08 mr1347 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
vg0429867566 NA 4.98E-07 mr1354 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
vg0429867566 NA 5.14E-06 mr1531 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
vg0429867566 NA 1.07E-08 mr1565 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
vg0429867566 NA 3.56E-06 mr1062_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
vg0429867566 NA 5.83E-07 mr1127_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
vg0429867566 NA 2.01E-06 mr1169_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
vg0429867566 NA 6.08E-06 mr1169_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
vg0429867566 7.93E-08 5.63E-11 mr1174_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
vg0429867566 1.02E-09 2.85E-23 mr1174_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
vg0429867566 NA 3.83E-07 mr1243_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
vg0429867566 2.09E-08 8.75E-08 mr1347_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
vg0429867566 5.51E-10 9.42E-23 mr1347_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
vg0429867566 NA 5.25E-06 mr1354_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
vg0429867566 NA 6.98E-08 mr1406_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
vg0429867566 NA 1.13E-08 mr1539_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
vg0429867566 NA 8.41E-10 mr1540_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
vg0429867566 NA 8.28E-07 mr1558_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
vg0429867566 NA 4.02E-11 mr1565_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
vg0429867566 NA 7.67E-11 mr1565_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
vg0429867566 NA 1.24E-09 mr1732_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
vg0429867566 NA 1.80E-06 mr1781_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
vg0429867566 4.52E-06 4.51E-06 mr1914_2 Jap_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