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Detailed information for vg0826160404:

Variant ID: vg0826160404 (JBrowse)Variation Type: INDEL
Chromosome: chr08Position: 26160404
Reference Allele: GTCTCTTAACCGTAAAACCGGGTACGACTCAAlternative Allele: ATCTCTTAACCGTAAAACCGGGTACGACTCA,G
Primary Allele: GTCTCTTAACCGTAAAACCG GGTACGACTCASecondary Allele: ATCTCTTAACCGTAAAACCG GGTACGACTCA

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TACGGACGAATGACCGTACGATTTAGGACGACGACGAAGGCGGCGCCACGCGGAATAAGTTCACTTTGGGTCTCTCTATTTGTCGCCTAGTCCGATTTTC[GTCTCTTAACCGTAAAACCGGGTACGACTCA/ATCTCTTAACCGTAAAACCGGGTACGACTCA,G]
TCCCTCAATTTACTAAAACCAGGCAAATGAGATCCCTCGGCGGTTTTGAATGCGGTTTTGGCTGACGTGGCGCTTACATGGCTTGTCTGACTAGGTCTTC

Reverse complement sequence

GAAGACCTAGTCAGACAAGCCATGTAAGCGCCACGTCAGCCAAAACCGCATTCAAAACCGCCGAGGGATCTCATTTGCCTGGTTTTAGTAAATTGAGGGA[TGAGTCGTACCCGGTTTTACGGTTAAGAGAC/TGAGTCGTACCCGGTTTTACGGTTAAGAGAT,C]
GAAAATCGGACTAGGCGACAAATAGAGAGACCCAAAGTGAACTTATTCCGCGTGGCGCCGCCTTCGTCGTCGTCCTAAATCGTACGGTCATTCGTCCGTA

Allele Frequencies:

Populations Population SizeFrequency of GTCTCTTAACCGTAAAACCG GGTACGACTCA(primary allele) Frequency of ATCTCTTAACCGTAAAACCG GGTACGACTCA(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 89.30% 10.30% 0.36% 0.00% G: 0.04%
All Indica  2759 87.60% 11.90% 0.43% 0.00% G: 0.04%
All Japonica  1512 99.60% 0.10% 0.26% 0.00% G: 0.07%
Aus  269 43.50% 56.10% 0.37% 0.00% NA
Indica I  595 66.10% 33.40% 0.50% 0.00% NA
Indica II  465 96.60% 3.40% 0.00% 0.00% NA
Indica III  913 96.30% 3.50% 0.22% 0.00% NA
Indica Intermediate  786 88.50% 10.40% 0.89% 0.00% G: 0.13%
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.60% 0.00% 0.20% 0.00% G: 0.20%
Japonica Intermediate  241 98.30% 0.40% 1.24% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 93.30% 6.70% 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
vg0826160404 GTCTCTTAACCGTAAAACCGGGTACGACTCA -> ATCTCTTAACCGTAAAACCGGGTACGACTC A LOC_Os08g41420.1 upstream_gene_variant ; 2541.0bp to feature; MODIFIER silent_mutation Average:97.029; most accessible tissue: Minghui63 flower, score: 99.357 N N N N
vg0826160404 GTCTCTTAACCGTAAAACCGGGTACGACTCA -> ATCTCTTAACCGTAAAACCGGGTACGACTC A LOC_Os08g41440.1 downstream_gene_variant ; 4605.0bp to feature; MODIFIER silent_mutation Average:97.029; most accessible tissue: Minghui63 flower, score: 99.357 N N N N
vg0826160404 GTCTCTTAACCGTAAAACCGGGTACGACTCA -> ATCTCTTAACCGTAAAACCGGGTACGACTC A LOC_Os08g41430.1 intron_variant ; MODIFIER silent_mutation Average:97.029; most accessible tissue: Minghui63 flower, score: 99.357 N N N N
vg0826160404 GTCTCTTAACCGTAAAACCGGGTACGACTCA -> G LOC_Os08g41420.1 upstream_gene_variant ; 2542.0bp to feature; MODIFIER silent_mutation Average:97.029; most accessible tissue: Minghui63 flower, score: 99.357 N N N N
vg0826160404 GTCTCTTAACCGTAAAACCGGGTACGACTCA -> G LOC_Os08g41440.1 downstream_gene_variant ; 4604.0bp to feature; MODIFIER silent_mutation Average:97.029; most accessible tissue: Minghui63 flower, score: 99.357 N N N N
vg0826160404 GTCTCTTAACCGTAAAACCGGGTACGACTCA -> G LOC_Os08g41430.1 intron_variant ; MODIFIER silent_mutation Average:97.029; most accessible tissue: Minghui63 flower, score: 99.357 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)
vg0826160404 GTCTC* ATCTC* -0.01 -0.04 -0.03 -0.01 -0.01 -0.01
vg0826160404 GTCTC* G 0.1 0.08 0.09 0.04 0.06 0.05

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0826160404 NA 1.73E-06 mr1038 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
vg0826160404 NA 7.45E-06 mr1038 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
vg0826160404 5.72E-06 5.72E-06 mr1046 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
vg0826160404 NA 2.96E-06 mr1048 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
vg0826160404 7.82E-06 7.82E-06 mr1048 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
vg0826160404 4.45E-06 NA mr1139 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
vg0826160404 NA 4.52E-07 mr1209 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
vg0826160404 3.53E-06 5.06E-07 mr1280 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
vg0826160404 1.48E-07 1.53E-07 mr1280 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
vg0826160404 4.92E-06 8.77E-06 mr1283 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
vg0826160404 NA 7.95E-06 mr1288 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
vg0826160404 5.31E-06 5.31E-06 mr1288 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
vg0826160404 NA 4.62E-11 mr1307 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
vg0826160404 3.52E-06 3.52E-06 mr1307 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
vg0826160404 NA 3.93E-06 mr1337 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
vg0826160404 NA 3.78E-08 mr1389 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
vg0826160404 NA 1.55E-07 mr1389 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
vg0826160404 NA 3.94E-06 mr1433 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
vg0826160404 NA 9.22E-06 mr1511 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
vg0826160404 6.70E-06 6.70E-06 mr1576 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
vg0826160404 3.33E-07 1.04E-06 mr1775 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
vg0826160404 NA 7.39E-06 mr1884 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
vg0826160404 7.14E-07 6.02E-07 mr1920 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
vg0826160404 NA 4.12E-06 mr1931 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
vg0826160404 NA 1.10E-06 mr1038_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
vg0826160404 NA 4.98E-07 mr1038_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
vg0826160404 NA 2.53E-06 mr1389_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
vg0826160404 NA 9.05E-06 mr1874_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