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Detailed information for vg0401154727:

Variant ID: vg0401154727 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 1154727
Reference Allele: GAlternative Allele: T
Primary Allele: TSecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 82. )

Flanking Sequence (100 bp) in Reference Genome:


CATATAATTTATTTAATATTTTAAAAAGTACTCCTACTCTGTGATCATCGGTACCAACATGGCGTGGAATTTTAATGACCGCAGATACGTATATAGAGTA[G/T]
GGTTGTGTTTAGATCCAAAGTTTAGATCCAAATTTCAGTTCTTTTTCATCACATCAACCTATCATACACACACAACTTTTCAGTCATATCATCTTCAATT

Reverse complement sequence

AATTGAAGATGATATGACTGAAAAGTTGTGTGTGTATGATAGGTTGATGTGATGAAAAAGAACTGAAATTTGGATCTAAACTTTGGATCTAAACACAACC[C/A]
TACTCTATATACGTATCTGCGGTCATTAAAATTCCACGCCATGTTGGTACCGATGATCACAGAGTAGGAGTACTTTTTAAAATATTAAATAAATTATATG

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 46.80% 25.80% 2.16% 25.24% NA
All Indica  2759 68.70% 6.70% 2.57% 21.96% NA
All Japonica  1512 6.10% 60.50% 0.99% 32.41% NA
Aus  269 65.80% 6.30% 4.09% 23.79% NA
Indica I  595 76.00% 2.20% 3.70% 18.15% NA
Indica II  465 78.70% 14.20% 0.43% 6.67% NA
Indica III  913 62.10% 4.20% 1.86% 31.87% NA
Indica Intermediate  786 65.00% 8.80% 3.82% 22.39% NA
Temperate Japonica  767 5.90% 90.10% 0.13% 3.91% NA
Tropical Japonica  504 7.10% 24.60% 2.38% 65.87% NA
Japonica Intermediate  241 4.60% 41.50% 0.83% 53.11% NA
VI/Aromatic  96 10.40% 79.20% 3.12% 7.29% NA
Intermediate  90 43.30% 25.60% 2.22% 28.89% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0401154727 G -> DEL N N silent_mutation Average:93.886; most accessible tissue: Minghui63 root, score: 99.412 N N N N
vg0401154727 G -> T LOC_Os04g02910.1 upstream_gene_variant ; 2508.0bp to feature; MODIFIER silent_mutation Average:93.886; most accessible tissue: Minghui63 root, score: 99.412 N N N N
vg0401154727 G -> T LOC_Os04g02910.3 upstream_gene_variant ; 3300.0bp to feature; MODIFIER silent_mutation Average:93.886; most accessible tissue: Minghui63 root, score: 99.412 N N N N
vg0401154727 G -> T LOC_Os04g02910.4 upstream_gene_variant ; 2508.0bp to feature; MODIFIER silent_mutation Average:93.886; most accessible tissue: Minghui63 root, score: 99.412 N N N N
vg0401154727 G -> T LOC_Os04g02910-LOC_Os04g02920 intergenic_region ; MODIFIER silent_mutation Average:93.886; most accessible tissue: Minghui63 root, score: 99.412 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)
vg0401154727 G T 0.02 -0.03 -0.02 -0.03 -0.04 -0.04

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0401154727 NA 2.92E-06 mr1045_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
vg0401154727 NA 6.02E-07 mr1084_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
vg0401154727 NA 5.74E-08 mr1194_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
vg0401154727 NA 2.17E-06 mr1205_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
vg0401154727 NA 3.82E-09 mr1206_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
vg0401154727 NA 1.23E-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
vg0401154727 NA 1.58E-10 mr1229_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
vg0401154727 NA 5.27E-07 mr1250_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
vg0401154727 NA 5.59E-09 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
vg0401154727 NA 6.66E-07 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
vg0401154727 NA 2.08E-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
vg0401154727 NA 3.08E-07 mr1263_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
vg0401154727 NA 9.52E-06 mr1295_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
vg0401154727 NA 8.30E-08 mr1482_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
vg0401154727 NA 6.21E-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
vg0401154727 NA 3.20E-07 mr1521_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
vg0401154727 NA 9.66E-07 mr1555_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
vg0401154727 NA 2.97E-08 mr1596_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
vg0401154727 NA 3.39E-06 mr1668_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
vg0401154727 NA 4.62E-06 mr1723_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
vg0401154727 NA 7.55E-06 mr1729_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
vg0401154727 NA 5.16E-06 mr1739_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
vg0401154727 NA 2.30E-09 mr1746_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
vg0401154727 NA 9.36E-07 mr1751_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
vg0401154727 NA 3.92E-07 mr1763_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
vg0401154727 NA 2.23E-08 mr1800_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
vg0401154727 NA 1.23E-06 mr1844_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
vg0401154727 NA 3.12E-10 mr1880_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