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Detailed information for vg0726319060:

Variant ID: vg0726319060 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 26319060
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GGGGCCGGTAGAGCTCTCTCACAAAATGTACTAGAGTTGTGGAGTTGTGGAGCTGCCTAAACCCAGCTCCATCTCTTTGGTTCATTCTGTGAGAGAGCTC[C/T]
ACCCAGCTCCGTTCCTATTTTTAGTGGAGCTGAAACTGTTTGGCTGAGCTTTAGCTCTAACTCCAGAAGAAGTGGAGCTGAAATTGGAGGTGTGCCAAAC

Reverse complement sequence

GTTTGGCACACCTCCAATTTCAGCTCCACTTCTTCTGGAGTTAGAGCTAAAGCTCAGCCAAACAGTTTCAGCTCCACTAAAAATAGGAACGGAGCTGGGT[G/A]
GAGCTCTCTCACAGAATGAACCAAAGAGATGGAGCTGGGTTTAGGCAGCTCCACAACTCCACAACTCTAGTACATTTTGTGAGAGAGCTCTACCGGCCCC

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 82.30% 17.50% 0.21% 0.00% NA
All Indica  2759 98.90% 1.10% 0.07% 0.00% NA
All Japonica  1512 48.20% 51.30% 0.46% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 98.20% 1.80% 0.00% 0.00% NA
Indica II  465 99.60% 0.40% 0.00% 0.00% NA
Indica III  913 99.30% 0.50% 0.11% 0.00% NA
Indica Intermediate  786 98.50% 1.40% 0.13% 0.00% NA
Temperate Japonica  767 81.10% 18.10% 0.78% 0.00% NA
Tropical Japonica  504 7.70% 92.10% 0.20% 0.00% NA
Japonica Intermediate  241 28.20% 71.80% 0.00% 0.00% NA
VI/Aromatic  96 93.80% 6.20% 0.00% 0.00% NA
Intermediate  90 81.10% 17.80% 1.11% 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
vg0726319060 C -> T LOC_Os07g44030.1 upstream_gene_variant ; 4208.0bp to feature; MODIFIER silent_mutation Average:84.642; most accessible tissue: Zhenshan97 panicle, score: 97.353 N N N N
vg0726319060 C -> T LOC_Os07g44040.1 upstream_gene_variant ; 2147.0bp to feature; MODIFIER silent_mutation Average:84.642; most accessible tissue: Zhenshan97 panicle, score: 97.353 N N N N
vg0726319060 C -> T LOC_Os07g44030-LOC_Os07g44040 intergenic_region ; MODIFIER silent_mutation Average:84.642; most accessible tissue: Zhenshan97 panicle, score: 97.353 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)
vg0726319060 C T -0.03 0.03 0.01 0.04 0.01 -0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0726319060 NA 1.39E-06 mr1182 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
vg0726319060 NA 1.11E-06 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
vg0726319060 NA 3.09E-12 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
vg0726319060 4.41E-06 1.23E-14 mr1336 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
vg0726319060 NA 7.11E-07 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
vg0726319060 NA 1.96E-12 mr1579 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
vg0726319060 NA 6.03E-14 mr1701 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
vg0726319060 NA 2.74E-19 mr1715 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
vg0726319060 NA 2.46E-09 mr1137_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
vg0726319060 NA 2.71E-08 mr1180_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
vg0726319060 NA 3.77E-06 mr1182_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
vg0726319060 NA 2.12E-10 mr1338_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
vg0726319060 NA 2.81E-07 mr1338_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
vg0726319060 NA 5.48E-07 mr1418_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
vg0726319060 NA 1.11E-06 mr1488_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
vg0726319060 NA 6.21E-16 mr1715_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
vg0726319060 NA 1.16E-10 mr1851_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
vg0726319060 NA 2.01E-13 mr1864_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
vg0726319060 NA 7.94E-08 mr1966_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