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Detailed information for vg0721650261:

Variant ID: vg0721650261 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 21650261
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AAAACTAATTTGGTAATGTAAATATTACTATATTTGTCTATAAACTTAGTCAAACTTTAAGCAGATTGACTTTGACCAAAGTCAAAACATCTTGTAATCT[G/A]
AAACGGAGAGAGTGTACAGTATTATGATTCTACGATAAATTTTAGACTCGAGAACAAATTGAAGGACCTAAAGTAAACTTATTCCTACCGACTGTGGTAC

Reverse complement sequence

GTACCACAGTCGGTAGGAATAAGTTTACTTTAGGTCCTTCAATTTGTTCTCGAGTCTAAAATTTATCGTAGAATCATAATACTGTACACTCTCTCCGTTT[C/T]
AGATTACAAGATGTTTTGACTTTGGTCAAAGTCAATCTGCTTAAAGTTTGACTAAGTTTATAGACAAATATAGTAATATTTACATTACCAAATTAGTTTT

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 52.70% 46.50% 0.19% 0.63% NA
All Indica  2759 83.60% 15.00% 0.33% 1.05% NA
All Japonica  1512 0.20% 99.70% 0.00% 0.07% NA
Aus  269 57.20% 42.80% 0.00% 0.00% NA
Indica I  595 86.10% 13.60% 0.34% 0.00% NA
Indica II  465 89.00% 8.00% 0.86% 2.15% NA
Indica III  913 81.30% 18.30% 0.11% 0.33% NA
Indica Intermediate  786 81.20% 16.50% 0.25% 2.04% NA
Temperate Japonica  767 0.10% 99.70% 0.00% 0.13% NA
Tropical Japonica  504 0.00% 100.00% 0.00% 0.00% NA
Japonica Intermediate  241 0.80% 99.20% 0.00% 0.00% NA
VI/Aromatic  96 0.00% 100.00% 0.00% 0.00% NA
Intermediate  90 28.90% 71.10% 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
vg0721650261 G -> DEL N N silent_mutation Average:83.814; most accessible tissue: Callus, score: 97.392 N N N N
vg0721650261 G -> A LOC_Os07g36230.1 upstream_gene_variant ; 2993.0bp to feature; MODIFIER silent_mutation Average:83.814; most accessible tissue: Callus, score: 97.392 N N N N
vg0721650261 G -> A LOC_Os07g36230.3 upstream_gene_variant ; 3461.0bp to feature; MODIFIER silent_mutation Average:83.814; most accessible tissue: Callus, score: 97.392 N N N N
vg0721650261 G -> A LOC_Os07g36230.2 upstream_gene_variant ; 4382.0bp to feature; MODIFIER silent_mutation Average:83.814; most accessible tissue: Callus, score: 97.392 N N N N
vg0721650261 G -> A LOC_Os07g36230.4 upstream_gene_variant ; 4559.0bp to feature; MODIFIER silent_mutation Average:83.814; most accessible tissue: Callus, score: 97.392 N N N N
vg0721650261 G -> A LOC_Os07g36220-LOC_Os07g36230 intergenic_region ; MODIFIER silent_mutation Average:83.814; most accessible tissue: Callus, score: 97.392 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)
vg0721650261 G A 0.02 0.03 0.02 -0.01 0.0 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0721650261 NA 1.42E-30 mr1086 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
vg0721650261 NA 2.65E-06 mr1103 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
vg0721650261 NA 3.60E-07 mr1226 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
vg0721650261 NA 6.15E-06 mr1246 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
vg0721650261 NA 1.66E-07 mr1559 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
vg0721650261 NA 3.10E-06 mr1560 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
vg0721650261 NA 6.15E-10 mr1905 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
vg0721650261 NA 1.27E-11 mr1949 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
vg0721650261 1.55E-06 NA mr1036_2 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
vg0721650261 NA 2.29E-13 mr1128_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
vg0721650261 NA 1.41E-16 mr1148_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
vg0721650261 6.58E-06 NA mr1169_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
vg0721650261 NA 3.43E-09 mr1198_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
vg0721650261 NA 7.00E-08 mr1275_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
vg0721650261 NA 7.57E-07 mr1302_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
vg0721650261 NA 1.03E-26 mr1323_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
vg0721650261 NA 3.00E-23 mr1386_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
vg0721650261 NA 3.36E-08 mr1659_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
vg0721650261 NA 9.18E-08 mr1681_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
vg0721650261 NA 8.06E-06 mr1691_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
vg0721650261 NA 9.02E-11 mr1714_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
vg0721650261 5.59E-06 5.03E-12 mr1806_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
vg0721650261 NA 4.54E-06 mr1806_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
vg0721650261 NA 9.55E-07 mr1834_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
vg0721650261 NA 8.45E-09 mr1835_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
vg0721650261 NA 6.53E-32 mr1873_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
vg0721650261 NA 2.82E-12 mr1904_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