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Detailed information for vg0314728343:

Variant ID: vg0314728343 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 14728343
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TCACGATTTTTGATAAATTTTAATCGGTTTTTGATAAATTTCAACTGAAATTCGACCAAATATACTGTTTAACTTTTAAAATTTTAATCGAAACTTAATT[T/C]
CAAGCTGTATCCAAATTTCGTAAAACTCCATCAGTTTTCGTGGAAATTATGAACCCTGACCAGTACTAGCAGGAGCAGCAACCGCGCAACTACCCAGCAA

Reverse complement sequence

TTGCTGGGTAGTTGCGCGGTTGCTGCTCCTGCTAGTACTGGTCAGGGTTCATAATTTCCACGAAAACTGATGGAGTTTTACGAAATTTGGATACAGCTTG[A/G]
AATTAAGTTTCGATTAAAATTTTAAAAGTTAAACAGTATATTTGGTCGAATTTCAGTTGAAATTTATCAAAAACCGATTAAAATTTATCAAAAATCGTGA

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 57.80% 25.20% 4.80% 12.27% NA
All Indica  2759 66.00% 13.40% 2.97% 17.62% NA
All Japonica  1512 44.40% 46.60% 8.80% 0.20% NA
Aus  269 68.80% 0.40% 1.12% 29.74% NA
Indica I  595 57.30% 2.20% 4.37% 36.13% NA
Indica II  465 58.90% 1.50% 3.23% 36.34% NA
Indica III  913 69.00% 29.10% 0.33% 1.53% NA
Indica Intermediate  786 73.40% 10.60% 4.83% 11.20% NA
Temperate Japonica  767 71.30% 13.30% 15.25% 0.13% NA
Tropical Japonica  504 16.50% 82.30% 1.19% 0.00% NA
Japonica Intermediate  241 17.00% 78.00% 4.15% 0.83% NA
VI/Aromatic  96 14.60% 84.40% 1.04% 0.00% NA
Intermediate  90 42.20% 36.70% 8.89% 12.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0314728343 T -> C LOC_Os03g25720.1 upstream_gene_variant ; 3089.0bp to feature; MODIFIER silent_mutation Average:99.529; most accessible tissue: Minghui63 root, score: 99.793 N N N N
vg0314728343 T -> C LOC_Os03g25750.1 upstream_gene_variant ; 429.0bp to feature; MODIFIER silent_mutation Average:99.529; most accessible tissue: Minghui63 root, score: 99.793 N N N N
vg0314728343 T -> C LOC_Os03g25720-LOC_Os03g25750 intergenic_region ; MODIFIER silent_mutation Average:99.529; most accessible tissue: Minghui63 root, score: 99.793 N N N N
vg0314728343 T -> DEL N N silent_mutation Average:99.529; most accessible tissue: Minghui63 root, score: 99.793 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)
vg0314728343 T C -0.01 -0.01 -0.01 -0.02 -0.01 -0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0314728343 1.21E-06 7.82E-09 mr1045 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
vg0314728343 NA 2.63E-06 mr1077 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
vg0314728343 NA 9.10E-07 mr1202 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
vg0314728343 NA 3.34E-15 mr1330 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
vg0314728343 NA 2.32E-08 mr1330 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
vg0314728343 NA 8.89E-09 mr1332 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
vg0314728343 NA 1.10E-08 mr1338 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
vg0314728343 NA 4.43E-06 mr1338 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
vg0314728343 NA 1.80E-07 mr1359 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
vg0314728343 NA 1.68E-06 mr1448 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
vg0314728343 NA 2.59E-11 mr1486 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
vg0314728343 NA 2.92E-13 mr1521 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
vg0314728343 NA 2.73E-07 mr1521 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
vg0314728343 NA 7.18E-07 mr1527 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
vg0314728343 NA 5.09E-06 mr1548 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
vg0314728343 NA 6.12E-09 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
vg0314728343 NA 9.90E-09 mr1570 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
vg0314728343 NA 3.19E-20 mr1580 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
vg0314728343 NA 2.49E-07 mr1627 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
vg0314728343 NA 3.18E-07 mr1668 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
vg0314728343 NA 1.71E-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
vg0314728343 NA 3.85E-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
vg0314728343 NA 7.28E-06 mr1729 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
vg0314728343 NA 1.88E-08 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
vg0314728343 9.36E-06 NA mr1789 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
vg0314728343 NA 4.38E-07 mr1844 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
vg0314728343 NA 2.34E-06 mr1977 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
vg0314728343 NA 3.80E-10 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