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Detailed information for vg0502617682:

Variant ID: vg0502617682 (JBrowse)Variation Type: INDEL
Chromosome: chr05Position: 2617682
Reference Allele: AAlternative Allele: G,AAGG
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CTATTAATTAATATATTATTACTATGAATCTAGACATGTTCCTTATTACTGTGAATCTAGACATGTTCACTATCTATCCATATCCTAGTATTACAAATTT[A/G,AAGG]
AACATATTTCTATCTATATCTTAGTACTATGAATCTAGACATTTCCCTATCCAAATACTAGTATTACGAATTTAGGCATGTTCGCTATCCATGTCTTAGT

Reverse complement sequence

ACTAAGACATGGATAGCGAACATGCCTAAATTCGTAATACTAGTATTTGGATAGGGAAATGTCTAGATTCATAGTACTAAGATATAGATAGAAATATGTT[T/C,CCTT]
AAATTTGTAATACTAGGATATGGATAGATAGTGAACATGTCTAGATTCACAGTAATAAGGAACATGTCTAGATTCATAGTAATAATATATTAATTAATAG

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 82.20% 17.80% 0.04% 0.00% AAGG: 0.02%
All Indica  2759 98.00% 2.00% 0.00% 0.00% NA
All Japonica  1512 65.60% 34.30% 0.07% 0.00% NA
Aus  269 39.00% 61.00% 0.00% 0.00% NA
Indica I  595 99.70% 0.30% 0.00% 0.00% NA
Indica II  465 98.10% 1.90% 0.00% 0.00% NA
Indica III  913 97.20% 2.80% 0.00% 0.00% NA
Indica Intermediate  786 97.60% 2.40% 0.00% 0.00% NA
Temperate Japonica  767 96.60% 3.30% 0.13% 0.00% NA
Tropical Japonica  504 11.50% 88.50% 0.00% 0.00% NA
Japonica Intermediate  241 80.10% 19.90% 0.00% 0.00% NA
VI/Aromatic  96 16.70% 83.30% 0.00% 0.00% NA
Intermediate  90 74.40% 23.30% 1.11% 0.00% AAGG: 1.11%

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0502617682 A -> G LOC_Os05g05310.1 upstream_gene_variant ; 431.0bp to feature; MODIFIER silent_mutation Average:94.121; most accessible tissue: Callus, score: 98.864 N N N N
vg0502617682 A -> G LOC_Os05g05310.2 upstream_gene_variant ; 432.0bp to feature; MODIFIER silent_mutation Average:94.121; most accessible tissue: Callus, score: 98.864 N N N N
vg0502617682 A -> G LOC_Os05g05300.1 downstream_gene_variant ; 3597.0bp to feature; MODIFIER silent_mutation Average:94.121; most accessible tissue: Callus, score: 98.864 N N N N
vg0502617682 A -> G LOC_Os05g05320.1 downstream_gene_variant ; 485.0bp to feature; MODIFIER silent_mutation Average:94.121; most accessible tissue: Callus, score: 98.864 N N N N
vg0502617682 A -> G LOC_Os05g05320.2 downstream_gene_variant ; 2421.0bp to feature; MODIFIER silent_mutation Average:94.121; most accessible tissue: Callus, score: 98.864 N N N N
vg0502617682 A -> G LOC_Os05g05310-LOC_Os05g05320 intergenic_region ; MODIFIER silent_mutation Average:94.121; most accessible tissue: Callus, score: 98.864 N N N N
vg0502617682 A -> AAGG LOC_Os05g05310.1 upstream_gene_variant ; 432.0bp to feature; MODIFIER silent_mutation Average:94.121; most accessible tissue: Callus, score: 98.864 N N N N
vg0502617682 A -> AAGG LOC_Os05g05310.2 upstream_gene_variant ; 433.0bp to feature; MODIFIER silent_mutation Average:94.121; most accessible tissue: Callus, score: 98.864 N N N N
vg0502617682 A -> AAGG LOC_Os05g05300.1 downstream_gene_variant ; 3598.0bp to feature; MODIFIER silent_mutation Average:94.121; most accessible tissue: Callus, score: 98.864 N N N N
vg0502617682 A -> AAGG LOC_Os05g05320.1 downstream_gene_variant ; 484.0bp to feature; MODIFIER silent_mutation Average:94.121; most accessible tissue: Callus, score: 98.864 N N N N
vg0502617682 A -> AAGG LOC_Os05g05320.2 downstream_gene_variant ; 2420.0bp to feature; MODIFIER silent_mutation Average:94.121; most accessible tissue: Callus, score: 98.864 N N N N
vg0502617682 A -> AAGG LOC_Os05g05310-LOC_Os05g05320 intergenic_region ; MODIFIER silent_mutation Average:94.121; most accessible tissue: Callus, score: 98.864 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)
vg0502617682 A AAGG -0.04 0.03 0.08 0.03 0.01 0.03
vg0502617682 A G -0.01 -0.02 -0.02 -0.01 -0.01 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0502617682 NA 7.56E-13 Grain_width 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
vg0502617682 NA 9.45E-06 mr1295 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
vg0502617682 NA 3.45E-06 mr1398 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
vg0502617682 NA 1.93E-12 mr1410 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
vg0502617682 NA 8.28E-06 mr1543 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
vg0502617682 NA 2.78E-08 mr1549 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
vg0502617682 NA 9.25E-08 mr1551 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
vg0502617682 NA 1.89E-11 mr1593 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
vg0502617682 NA 1.52E-18 mr1593 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
vg0502617682 NA 1.56E-12 mr1696 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
vg0502617682 NA 6.02E-07 mr1723 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
vg0502617682 NA 2.35E-07 mr1733 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
vg0502617682 NA 8.54E-08 mr1757 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
vg0502617682 NA 1.68E-06 mr1097_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
vg0502617682 NA 2.84E-07 mr1121_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
vg0502617682 NA 1.40E-07 mr1250_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
vg0502617682 NA 2.25E-07 mr1295_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
vg0502617682 NA 2.61E-13 mr1410_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
vg0502617682 NA 6.30E-07 mr1495_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
vg0502617682 NA 9.95E-06 mr1498_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
vg0502617682 NA 1.58E-16 mr1593_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
vg0502617682 NA 7.72E-32 mr1593_2 Jap_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
vg0502617682 NA 1.28E-07 mr1679_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
vg0502617682 NA 1.76E-07 mr1696_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
vg0502617682 NA 9.65E-19 mr1699_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
vg0502617682 NA 8.92E-09 mr1733_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
vg0502617682 NA 1.26E-06 mr1786_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
vg0502617682 NA 4.51E-06 mr1936_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
vg0502617682 NA 9.38E-12 mr1993_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