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Detailed information for vg1125897494:

Variant ID: vg1125897494 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 25897494
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTTCTAAACATAATTTGCCAAAATTTCAAATTAAGGCTGTGTTGAGTTCACATTAAAATTGGAAGTTTGGTTGAAATTGGAACGATGTGACGAAAAAGTT[G/A]
GAAGTTTGTGTGTGTAGGAAAGTTTTGATGTGATAGAAAAGTTTGAAGTTTGAAGAAAAAATTTTACAACTAAACACGGCCTAAATCAATACATAATTCA

Reverse complement sequence

TGAATTATGTATTGATTTAGGCCGTGTTTAGTTGTAAAATTTTTTCTTCAAACTTCAAACTTTTCTATCACATCAAAACTTTCCTACACACACAAACTTC[C/T]
AACTTTTTCGTCACATCGTTCCAATTTCAACCAAACTTCCAATTTTAATGTGAACTCAACACAGCCTTAATTTGAAATTTTGGCAAATTATGTTTAGAAA

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 91.30% 8.60% 0.08% 0.00% NA
All Indica  2759 87.00% 13.00% 0.04% 0.00% NA
All Japonica  1512 98.60% 1.20% 0.20% 0.00% NA
Aus  269 93.30% 6.70% 0.00% 0.00% NA
Indica I  595 68.10% 31.90% 0.00% 0.00% NA
Indica II  465 83.00% 16.80% 0.22% 0.00% NA
Indica III  913 95.90% 4.10% 0.00% 0.00% NA
Indica Intermediate  786 93.30% 6.70% 0.00% 0.00% NA
Temperate Japonica  767 98.00% 1.60% 0.39% 0.00% NA
Tropical Japonica  504 98.80% 1.20% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 88.90% 11.10% 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
vg1125897494 G -> A LOC_Os11g42960.1 upstream_gene_variant ; 2462.0bp to feature; MODIFIER silent_mutation Average:82.455; most accessible tissue: Zhenshan97 root, score: 98.87 N N N N
vg1125897494 G -> A LOC_Os11g42970.1 upstream_gene_variant ; 275.0bp to feature; MODIFIER silent_mutation Average:82.455; most accessible tissue: Zhenshan97 root, score: 98.87 N N N N
vg1125897494 G -> A LOC_Os11g42970-LOC_Os11g42980 intergenic_region ; MODIFIER silent_mutation Average:82.455; most accessible tissue: Zhenshan97 root, score: 98.87 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)
vg1125897494 G A 0.03 0.02 -0.01 0.02 0.01 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1125897494 2.95E-15 1.02E-23 mr1191 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
vg1125897494 1.09E-18 3.17E-21 mr1191 Ind_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
vg1125897494 1.92E-18 2.13E-26 mr1644 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
vg1125897494 1.01E-19 7.37E-22 mr1644 Ind_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
vg1125897494 1.21E-06 6.04E-10 mr1662 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
vg1125897494 2.31E-06 7.60E-10 mr1662 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
vg1125897494 1.66E-19 1.33E-37 mr1191_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
vg1125897494 4.66E-22 4.26E-30 mr1191_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
vg1125897494 NA 1.83E-06 mr1530_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
vg1125897494 NA 8.29E-10 mr1662_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
vg1125897494 NA 8.39E-10 mr1662_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
vg1125897494 NA 8.20E-09 mr1745_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