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Detailed information for vg1013422858:

Variant ID: vg1013422858 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 13422858
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TCACACCGTTCTTGTTCCATAGTCTTCACTACGGGTTTCGGCAGATTTGGTCAAAGGGCCTCATGCCATCCGCCTACAGTTACCTACGGTCGTTTTTCTA[A/G]
TCAGCACCAATGATCTTTTTTATATAGTTGTGTATTTTATGTCCACGACATATAACTTAATATTCCACTAATGATCTGATTGATTTTTTAGACAGATCAA

Reverse complement sequence

TTGATCTGTCTAAAAAATCAATCAGATCATTAGTGGAATATTAAGTTATATGTCGTGGACATAAAATACACAACTATATAAAAAAGATCATTGGTGCTGA[T/C]
TAGAAAAACGACCGTAGGTAACTGTAGGCGGATGGCATGAGGCCCTTTGACCAAATCTGCCGAAACCCGTAGTGAAGACTATGGAACAAGAACGGTGTGA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 91.60% 6.30% 2.14% 0.00% NA
All Indica  2759 99.50% 0.50% 0.04% 0.00% NA
All Japonica  1512 80.80% 13.10% 6.08% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 98.50% 1.30% 0.22% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 99.20% 0.80% 0.00% 0.00% NA
Temperate Japonica  767 89.80% 1.40% 8.74% 0.00% NA
Tropical Japonica  504 69.00% 28.60% 2.38% 0.00% NA
Japonica Intermediate  241 76.80% 17.80% 5.39% 0.00% NA
VI/Aromatic  96 19.80% 75.00% 5.21% 0.00% NA
Intermediate  90 82.20% 14.40% 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
vg1013422858 A -> G LOC_Os10g25900.1 3_prime_UTR_variant ; 262.0bp to feature; MODIFIER silent_mutation Average:61.579; most accessible tissue: Zhenshan97 root, score: 89.337 N N N N
vg1013422858 A -> G LOC_Os10g25890.1 upstream_gene_variant ; 1594.0bp to feature; MODIFIER silent_mutation Average:61.579; most accessible tissue: Zhenshan97 root, score: 89.337 N N N N
vg1013422858 A -> G LOC_Os10g25910.1 downstream_gene_variant ; 4988.0bp to feature; MODIFIER silent_mutation Average:61.579; most accessible tissue: Zhenshan97 root, score: 89.337 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)
vg1013422858 A G -0.02 0.0 0.0 0.01 0.02 0.03

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1013422858 5.89E-06 NA mr1030 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
vg1013422858 NA 3.16E-07 mr1220 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
vg1013422858 2.72E-06 NA mr1301 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
vg1013422858 NA 3.78E-09 mr1332 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
vg1013422858 NA 5.77E-06 mr1425 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
vg1013422858 NA 7.39E-06 mr1428 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
vg1013422858 NA 6.92E-07 mr1438 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
vg1013422858 NA 3.15E-06 mr1470 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
vg1013422858 4.15E-06 NA mr1533 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
vg1013422858 NA 5.02E-11 mr1570 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
vg1013422858 NA 3.08E-06 mr1596 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
vg1013422858 3.48E-06 3.48E-06 mr1877_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