Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0723310247:

Variant ID: vg0723310247 (JBrowse)Variation Type: INDEL
Chromosome: chr07Position: 23310247
Reference Allele: AAlternative Allele: T,ATGGATGCATGATAGTAACAAAAAATCGT
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CCATCTCGTTTTGCGTAAAAAACTTAATCTTCATCTTTAGGATAAAAGAACACCACCAAAGTATATATATTTTGAGACGGGAAGGAGTAACAAAAAATCG[A/T,ATGGATGCATGATAGTAACAAAAAATCGT]
TGCATGGATGCATGATGTTTAGATTCCCTGTGACCAATTGTATACTTGATTTAGGTAAGGAATAAGTTCACGTTAACTCTCTCAAATATATGTCGGATTT

Reverse complement sequence

AAATCCGACATATATTTGAGAGAGTTAACGTGAACTTATTCCTTACCTAAATCAAGTATACAATTGGTCACAGGGAATCTAAACATCATGCATCCATGCA[T/A,ACGATTTTTTGTTACTATCATGCATCCAT]
CGATTTTTTGTTACTCCTTCCCGTCTCAAAATATATATACTTTGGTGGTGTTCTTTTATCCTAAAGATGAAGATTAAGTTTTTTACGCAAAACGAGATGG

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 87.70% 11.20% 0.57% 0.00% ATGGATGCATGATAGTAACAAAAAATCGT: 0.49%
All Indica  2759 99.30% 0.50% 0.11% 0.00% NA
All Japonica  1512 64.70% 32.20% 1.52% 0.00% ATGGATGCATGATAGTAACAAAAAATCGT: 1.52%
Aus  269 98.10% 1.90% 0.00% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 97.60% 2.40% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.20% 0.40% 0.38% 0.00% NA
Temperate Japonica  767 39.20% 58.50% 1.96% 0.00% ATGGATGCATGATAGTAACAAAAAATCGT: 0.26%
Tropical Japonica  504 97.80% 1.40% 0.60% 0.00% ATGGATGCATGATAGTAACAAAAAATCGT: 0.20%
Japonica Intermediate  241 76.80% 12.90% 2.07% 0.00% ATGGATGCATGATAGTAACAAAAAATCGT: 8.30%
VI/Aromatic  96 88.50% 11.50% 0.00% 0.00% NA
Intermediate  90 84.40% 14.40% 1.11% 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
vg0723310247 A -> ATGGATGCATGATAGTAACAAAAAATCGT LOC_Os07g38860.1 upstream_gene_variant ; 4234.0bp to feature; MODIFIER silent_mutation Average:78.275; most accessible tissue: Zhenshan97 young leaf, score: 93.129 N N N N
vg0723310247 A -> ATGGATGCATGATAGTAACAAAAAATCGT LOC_Os07g38850.1 downstream_gene_variant ; 1270.0bp to feature; MODIFIER silent_mutation Average:78.275; most accessible tissue: Zhenshan97 young leaf, score: 93.129 N N N N
vg0723310247 A -> ATGGATGCATGATAGTAACAAAAAATCGT LOC_Os07g38850-LOC_Os07g38860 intergenic_region ; MODIFIER silent_mutation Average:78.275; most accessible tissue: Zhenshan97 young leaf, score: 93.129 N N N N
vg0723310247 A -> T LOC_Os07g38860.1 upstream_gene_variant ; 4235.0bp to feature; MODIFIER silent_mutation Average:78.275; most accessible tissue: Zhenshan97 young leaf, score: 93.129 N N N N
vg0723310247 A -> T LOC_Os07g38850.1 downstream_gene_variant ; 1269.0bp to feature; MODIFIER silent_mutation Average:78.275; most accessible tissue: Zhenshan97 young leaf, score: 93.129 N N N N
vg0723310247 A -> T LOC_Os07g38850-LOC_Os07g38860 intergenic_region ; MODIFIER silent_mutation Average:78.275; most accessible tissue: Zhenshan97 young leaf, score: 93.129 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)
vg0723310247 A ATGGA* 0.32 0.53 0.26 0.14 0.34 0.49
vg0723310247 A T -0.06 -0.05 -0.04 -0.03 -0.03 -0.03

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0723310247 NA 1.90E-07 mr1343 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
vg0723310247 2.64E-07 NA mr1354 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
vg0723310247 NA 1.15E-06 mr1354 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
vg0723310247 8.20E-06 6.78E-10 mr1829 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
vg0723310247 NA 1.58E-15 mr1902 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
vg0723310247 NA 3.47E-06 mr1902 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
vg0723310247 NA 7.95E-11 mr1011_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
vg0723310247 NA 1.97E-09 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
vg0723310247 NA 8.04E-07 mr1045_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
vg0723310247 NA 1.22E-06 mr1229_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
vg0723310247 NA 5.36E-08 mr1252_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
vg0723310247 NA 9.76E-06 mr1252_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
vg0723310247 NA 1.58E-09 mr1486_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
vg0723310247 1.43E-07 NA mr1563_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
vg0723310247 NA 2.95E-12 mr1563_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
vg0723310247 NA 2.61E-06 mr1693_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
vg0723310247 NA 8.26E-08 mr1748_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
vg0723310247 NA 8.76E-07 mr1754_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
vg0723310247 3.26E-06 3.26E-06 mr1754_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
vg0723310247 NA 5.78E-07 mr1780_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
vg0723310247 NA 5.37E-06 mr1785_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
vg0723310247 7.98E-08 1.94E-12 mr1829_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
vg0723310247 NA 5.60E-06 mr1829_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
vg0723310247 NA 4.18E-07 mr1865_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
vg0723310247 NA 4.96E-07 mr1880_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
vg0723310247 1.06E-08 1.41E-21 mr1902_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
vg0723310247 NA 1.16E-07 mr1902_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