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Detailed information for vg0604882318:

Variant ID: vg0604882318 (JBrowse)Variation Type: INDEL
Chromosome: chr06Position: 4882318
Reference Allele: ATAlternative Allele: GT,TT,A
Primary Allele: ATSecondary Allele: GT

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CGAAGGTGTCAGCGCCAGTGTCATCGGCGTTAACCGTTAAGACATTGAACGTTGGCGCGAATAATCCTAGTGTAAAAAAAATGGTTCATTTCTGAAATAA[AT/GT,TT,A]
TTTTTTTTCCAGAAGCCTATTCATAAAATAAGTTATTTTTCAAAAAGAATCAAAACGTAGAAATCTAGAGTGACGATTTGTCTGTCAAAGTGTCAAGCAC

Reverse complement sequence

GTGCTTGACACTTTGACAGACAAATCGTCACTCTAGATTTCTACGTTTTGATTCTTTTTGAAAAATAACTTATTTTATGAATAGGCTTCTGGAAAAAAAA[AT/AC,AA,T]
TTATTTCAGAAATGAACCATTTTTTTTACACTAGGATTATTCGCGCCAACGTTCAATGTCTTAACGGTTAACGCCGATGACACTGGCGCTGACACCTTCG

Allele Frequencies:

Populations Population SizeFrequency of AT(primary allele) Frequency of GT(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 39.20% 36.50% 15.38% 8.82% A: 0.02%
All Indica  2759 23.10% 58.00% 10.58% 8.26% NA
All Japonica  1512 66.40% 5.60% 19.51% 8.47% NA
Aus  269 45.70% 3.00% 34.94% 16.36% NA
Indica I  595 30.30% 64.40% 4.20% 1.18% NA
Indica II  465 31.00% 28.80% 21.29% 18.92% NA
Indica III  913 12.30% 74.60% 7.12% 6.02% NA
Indica Intermediate  786 25.70% 51.30% 13.10% 9.92% NA
Temperate Japonica  767 86.70% 2.20% 9.78% 1.30% NA
Tropical Japonica  504 39.70% 11.10% 30.16% 19.05% NA
Japonica Intermediate  241 57.70% 5.00% 28.22% 9.13% NA
VI/Aromatic  96 59.40% 0.00% 28.12% 11.46% A: 1.04%
Intermediate  90 35.60% 36.70% 21.11% 6.67% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0604882318 AT -> TT LOC_Os06g09580.1 upstream_gene_variant ; 4426.0bp to feature; MODIFIER N Average:81.846; most accessible tissue: Callus, score: 94.486 N N N N
vg0604882318 AT -> TT LOC_Os06g09600.1 downstream_gene_variant ; 3626.0bp to feature; MODIFIER N Average:81.846; most accessible tissue: Callus, score: 94.486 N N N N
vg0604882318 AT -> TT LOC_Os06g09580-LOC_Os06g09600 intergenic_region ; MODIFIER N Average:81.846; most accessible tissue: Callus, score: 94.486 N N N N
vg0604882318 AT -> A LOC_Os06g09580.1 upstream_gene_variant ; 4427.0bp to feature; MODIFIER silent_mutation Average:81.846; most accessible tissue: Callus, score: 94.486 N N N N
vg0604882318 AT -> A LOC_Os06g09600.1 downstream_gene_variant ; 3625.0bp to feature; MODIFIER silent_mutation Average:81.846; most accessible tissue: Callus, score: 94.486 N N N N
vg0604882318 AT -> A LOC_Os06g09580-LOC_Os06g09600 intergenic_region ; MODIFIER silent_mutation Average:81.846; most accessible tissue: Callus, score: 94.486 N N N N
vg0604882318 AT -> DEL N N silent_mutation Average:81.846; most accessible tissue: Callus, score: 94.486 N N N N
vg0604882318 AT -> GT LOC_Os06g09580.1 upstream_gene_variant ; 4426.0bp to feature; MODIFIER silent_mutation Average:81.846; most accessible tissue: Callus, score: 94.486 N N N N
vg0604882318 AT -> GT LOC_Os06g09600.1 downstream_gene_variant ; 3626.0bp to feature; MODIFIER silent_mutation Average:81.846; most accessible tissue: Callus, score: 94.486 N N N N
vg0604882318 AT -> GT LOC_Os06g09580-LOC_Os06g09600 intergenic_region ; MODIFIER silent_mutation Average:81.846; most accessible tissue: Callus, score: 94.486 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)
vg0604882318 AT A -0.23 -0.11 -0.03 -0.21 -0.18 -0.18
vg0604882318 AT GT -0.02 -0.04 -0.03 -0.02 -0.02 -0.02
vg0604882318 AT TT 0.02 0.02 0.01 0.01 0.02 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0604882318 NA 1.73E-11 Plant_height Jap_All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0604882318 NA 5.19E-06 mr1002 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
vg0604882318 5.09E-07 7.40E-29 mr1137 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
vg0604882318 3.06E-06 1.00E-15 mr1137 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
vg0604882318 5.84E-07 1.65E-15 mr1182 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
vg0604882318 NA 1.64E-07 mr1182 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
vg0604882318 NA 1.05E-06 mr1183 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
vg0604882318 NA 1.80E-10 mr1282 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
vg0604882318 NA 9.16E-06 mr1282 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
vg0604882318 NA 2.42E-06 mr1330 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
vg0604882318 NA 3.00E-06 mr1503 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
vg0604882318 NA 2.25E-11 mr1617 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
vg0604882318 3.57E-06 1.39E-13 mr1650 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
vg0604882318 NA 8.00E-06 mr1650 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
vg0604882318 NA 6.60E-10 mr1658 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
vg0604882318 NA 3.82E-08 mr1010_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
vg0604882318 NA 2.63E-06 mr1011_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
vg0604882318 4.96E-08 5.78E-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
vg0604882318 5.10E-07 6.21E-17 mr1137_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
vg0604882318 NA 1.08E-14 mr1182_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
vg0604882318 NA 1.16E-07 mr1182_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
vg0604882318 NA 4.91E-10 mr1282_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
vg0604882318 NA 4.65E-07 mr1330_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
vg0604882318 NA 1.47E-10 mr1530_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
vg0604882318 NA 1.28E-09 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