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Detailed information for vg0608112196:

Variant ID: vg0608112196 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 8112196
Reference Allele: CAlternative Allele: G
Primary Allele: CSecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TGAGCTGGATTAGTCAGCAAGGTGATCTCCATCACCTGTGTACGTGCTGGATAGTGGATTAGTTGGCCATGTTCTTGTCTCCTTTTGGATTTCGGATTTT[C/G]
ATTTGTATATTTTTCAAGCTTCTAAACGATGTGTTGTAAGAAAAATTTAAATAATTCTTTTTAGTATTTTTTTTAAAACAATCTTTTCACTCTATAGGTG

Reverse complement sequence

CACCTATAGAGTGAAAAGATTGTTTTAAAAAAAATACTAAAAAGAATTATTTAAATTTTTCTTACAACACATCGTTTAGAAGCTTGAAAAATATACAAAT[G/C]
AAAATCCGAAATCCAAAAGGAGACAAGAACATGGCCAACTAATCCACTATCCAGCACGTACACAGGTGATGGAGATCACCTTGCTGACTAATCCAGCTCA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 88.90% 8.30% 2.81% 0.00% NA
All Indica  2759 99.90% 0.10% 0.04% 0.00% NA
All Japonica  1512 66.30% 25.10% 8.60% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.70% 0.10% 0.13% 0.00% NA
Temperate Japonica  767 63.90% 27.00% 9.13% 0.00% NA
Tropical Japonica  504 81.50% 13.70% 4.76% 0.00% NA
Japonica Intermediate  241 41.90% 43.20% 14.94% 0.00% NA
VI/Aromatic  96 94.80% 5.20% 0.00% 0.00% NA
Intermediate  90 93.30% 4.40% 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
vg0608112196 C -> G LOC_Os06g14450.1 upstream_gene_variant ; 4053.0bp to feature; MODIFIER silent_mutation Average:79.73; most accessible tissue: Minghui63 flag leaf, score: 97.1 N N N N
vg0608112196 C -> G LOC_Os06g14450.2 upstream_gene_variant ; 4053.0bp to feature; MODIFIER silent_mutation Average:79.73; most accessible tissue: Minghui63 flag leaf, score: 97.1 N N N N
vg0608112196 C -> G LOC_Os06g14450.3 upstream_gene_variant ; 4053.0bp to feature; MODIFIER silent_mutation Average:79.73; most accessible tissue: Minghui63 flag leaf, score: 97.1 N N N N
vg0608112196 C -> G LOC_Os06g14440-LOC_Os06g14450 intergenic_region ; MODIFIER silent_mutation Average:79.73; most accessible tissue: Minghui63 flag leaf, score: 97.1 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)
vg0608112196 C G -0.01 0.0 0.0 -0.01 0.0 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0608112196 NA 1.76E-07 mr1002 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
vg0608112196 NA 2.16E-06 mr1002 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
vg0608112196 1.15E-07 NA mr1354 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
vg0608112196 NA 2.70E-09 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
vg0608112196 NA 1.32E-07 mr1030_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
vg0608112196 NA 2.22E-06 mr1097_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
vg0608112196 NA 2.69E-06 mr1354_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
vg0608112196 NA 6.69E-06 mr1549_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
vg0608112196 NA 9.65E-06 mr1567_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
vg0608112196 NA 2.75E-08 mr1568_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
vg0608112196 7.37E-09 3.74E-26 mr1679_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
vg0608112196 NA 1.06E-09 mr1679_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
vg0608112196 NA 1.13E-06 mr1757_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
vg0608112196 4.14E-08 2.23E-09 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
vg0608112196 NA 4.16E-07 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
vg0608112196 3.32E-07 NA 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
vg0608112196 NA 1.75E-06 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