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Detailed information for vg0909268786:

Variant ID: vg0909268786 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 9268786
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TAGTAGCTCCCAGGGCGAATCATAAACTGTCATTTAAGTATTTTGGACCTTTCATGTTTTCGAGAAGTTGGGTTCAGTGGCTTACAGGTTGCAGCTTCCT[A/G]
AATCCAGTACTATACATCCTGTATTCCATGTTTCTCAGCTCAAGGGTGCTAAGGATTTCCAACCACCAGTGTTGTCCGACCTGCCTGGCCCTAACCAAGA

Reverse complement sequence

TCTTGGTTAGGGCCAGGCAGGTCGGACAACACTGGTGGTTGGAAATCCTTAGCACCCTTGAGCTGAGAAACATGGAATACAGGATGTATAGTACTGGATT[T/C]
AGGAAGCTGCAACCTGTAAGCCACTGAACCCAACTTCTCGAAAACATGAAAGGTCCAAAATACTTAAATGACAGTTTATGATTCGCCCTGGGAGCTACTA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 58.90% 29.00% 0.51% 11.60% NA
All Indica  2759 79.20% 5.50% 0.40% 14.90% NA
All Japonica  1512 23.30% 76.50% 0.13% 0.07% NA
Aus  269 69.50% 2.20% 3.35% 24.91% NA
Indica I  595 76.50% 5.70% 0.17% 17.65% NA
Indica II  465 90.30% 1.50% 0.86% 7.31% NA
Indica III  913 73.40% 8.90% 0.55% 17.20% NA
Indica Intermediate  786 81.30% 3.90% 0.13% 14.63% NA
Temperate Japonica  767 18.10% 81.90% 0.00% 0.00% NA
Tropical Japonica  504 23.60% 76.00% 0.40% 0.00% NA
Japonica Intermediate  241 39.00% 60.60% 0.00% 0.41% NA
VI/Aromatic  96 19.80% 18.80% 0.00% 61.46% NA
Intermediate  90 46.70% 40.00% 2.22% 11.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0909268786 A -> G LOC_Os09g15250.1 synonymous_variant ; p.Leu324Leu; LOW synonymous_codon Average:71.122; most accessible tissue: Zhenshan97 root, score: 91.601 N N N N
vg0909268786 A -> DEL LOC_Os09g15250.1 N frameshift_variant Average:71.122; most accessible tissue: Zhenshan97 root, score: 91.601 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)
vg0909268786 A G 0.02 0.0 0.0 0.01 0.01 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0909268786 NA 4.39E-33 mr1137_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
vg0909268786 NA 9.01E-06 mr1298_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
vg0909268786 NA 1.52E-06 mr1318_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
vg0909268786 NA 1.89E-11 mr1377_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
vg0909268786 7.50E-07 2.68E-32 mr1617_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
vg0909268786 NA 6.83E-07 mr1617_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
vg0909268786 NA 1.24E-06 mr1702_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
vg0909268786 NA 1.61E-10 mr1705_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
vg0909268786 NA 1.66E-14 mr1713_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
vg0909268786 NA 5.39E-06 mr1713_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
vg0909268786 NA 5.76E-06 mr1729_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
vg0909268786 NA 4.55E-09 mr1783_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
vg0909268786 NA 8.16E-07 mr1785_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
vg0909268786 NA 3.13E-06 mr1788_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
vg0909268786 NA 3.49E-08 mr1804_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
vg0909268786 NA 3.56E-07 mr1819_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