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Detailed information for vg0306330280:

Variant ID: vg0306330280 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 6330280
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GGTCCAATACATACTAATTATCTAATTATTGACTAATATATTAATTAATATAGTGTAATTTATATAGGATTTGAATAATCTACCCGGTATCTTGTGACAC[C/T]
GGATAGTATAACCTAGGCACGCCCCTGGGTGTGCTACGGGAAACATTTTCTGAATCTTTGAAATGCCCACTAGCTCTCTCTGTGACATGCATGCTTGGAC

Reverse complement sequence

GTCCAAGCATGCATGTCACAGAGAGAGCTAGTGGGCATTTCAAAGATTCAGAAAATGTTTCCCGTAGCACACCCAGGGGCGTGCCTAGGTTATACTATCC[G/A]
GTGTCACAAGATACCGGGTAGATTATTCAAATCCTATATAAATTACACTATATTAATTAATATATTAGTCAATAATTAGATAATTAGTATGTATTGGACC

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 89.00% 10.10% 0.85% 0.00% NA
All Indica  2759 100.00% 0.00% 0.04% 0.00% NA
All Japonica  1512 66.40% 31.20% 2.45% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.80% 0.00% 0.17% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 43.90% 51.90% 4.17% 0.00% NA
Tropical Japonica  504 98.20% 1.60% 0.20% 0.00% NA
Japonica Intermediate  241 71.40% 27.00% 1.66% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 90.00% 7.80% 2.22% 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
vg0306330280 C -> T LOC_Os03g12064.5 upstream_gene_variant ; 2204.0bp to feature; MODIFIER silent_mutation Average:85.635; most accessible tissue: Minghui63 young leaf, score: 94.061 N N N N
vg0306330280 C -> T LOC_Os03g12064.4 upstream_gene_variant ; 3554.0bp to feature; MODIFIER silent_mutation Average:85.635; most accessible tissue: Minghui63 young leaf, score: 94.061 N N N N
vg0306330280 C -> T LOC_Os03g12064.1 intron_variant ; MODIFIER silent_mutation Average:85.635; most accessible tissue: Minghui63 young leaf, score: 94.061 N N N N
vg0306330280 C -> T LOC_Os03g12064.2 intron_variant ; MODIFIER silent_mutation Average:85.635; most accessible tissue: Minghui63 young leaf, score: 94.061 N N N N
vg0306330280 C -> T LOC_Os03g12064.3 intron_variant ; MODIFIER silent_mutation Average:85.635; most accessible tissue: Minghui63 young leaf, score: 94.061 N N N N
vg0306330280 C -> T LOC_Os03g12064.6 intron_variant ; MODIFIER silent_mutation Average:85.635; most accessible tissue: Minghui63 young leaf, score: 94.061 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)
vg0306330280 C T 0.0 0.0 0.0 0.01 0.02 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0306330280 NA 1.80E-07 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
vg0306330280 9.83E-07 NA mr1210 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
vg0306330280 NA 1.05E-07 mr1252 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
vg0306330280 NA 4.41E-06 mr1280 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
vg0306330280 8.67E-07 NA mr1305 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
vg0306330280 NA 5.03E-08 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
vg0306330280 1.16E-06 NA mr1585 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
vg0306330280 NA 9.97E-07 mr1585 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
vg0306330280 NA 1.26E-06 mr1671 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
vg0306330280 NA 6.30E-07 mr1708 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
vg0306330280 NA 4.59E-06 mr1729 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
vg0306330280 NA 2.00E-06 mr1788 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
vg0306330280 5.53E-06 5.52E-06 mr1811 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
vg0306330280 4.41E-06 4.41E-06 mr1812 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
vg0306330280 NA 1.83E-06 mr1880 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
vg0306330280 1.30E-06 NA mr1882 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
vg0306330280 NA 2.17E-07 mr1882 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
vg0306330280 NA 1.50E-07 mr1946 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