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Detailed information for vg0702957519:

Variant ID: vg0702957519 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 2957519
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GGCTGTGTTCGTTCCCAGTGGTTGGGAGCACTACCCTCCCGCACGGAAAATGAAACAGACCATTAACACGTGATTAATTAAGTATTAGTTATTTTTTTTT[T/C]
AAAAATGGATCAATATGATTTTTTAAACAACTTTCATATAGAAACATTTTTTTTTCAAAAAACATACCGTTTAACAGTTTGAAAAGTGTGCGTGCGGAAA

Reverse complement sequence

TTTCCGCACGCACACTTTTCAAACTGTTAAACGGTATGTTTTTTGAAAAAAAAATGTTTCTATATGAAAGTTGTTTAAAAAATCATATTGATCCATTTTT[A/G]
AAAAAAAAATAACTAATACTTAATTAATCACGTGTTAATGGTCTGTTTCATTTTCCGTGCGGGAGGGTAGTGCTCCCAACCACTGGGAACGAACACAGCC

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 79.10% 13.10% 7.81% 0.00% NA
All Indica  2759 86.20% 6.20% 7.61% 0.00% NA
All Japonica  1512 61.70% 28.70% 9.59% 0.00% NA
Aus  269 94.40% 2.60% 2.97% 0.00% NA
Indica I  595 64.50% 16.60% 18.82% 0.00% NA
Indica II  465 88.00% 5.60% 6.45% 0.00% NA
Indica III  913 98.90% 0.90% 0.22% 0.00% NA
Indica Intermediate  786 86.80% 4.80% 8.40% 0.00% NA
Temperate Japonica  767 42.40% 43.80% 13.82% 0.00% NA
Tropical Japonica  504 90.90% 5.00% 4.17% 0.00% NA
Japonica Intermediate  241 62.20% 30.30% 7.47% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 83.30% 10.00% 6.67% 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
vg0702957519 T -> C LOC_Os07g06110.1 upstream_gene_variant ; 2718.0bp to feature; MODIFIER silent_mutation Average:90.653; most accessible tissue: Zhenshan97 panicle, score: 95.951 N N N N
vg0702957519 T -> C LOC_Os07g06100.1 downstream_gene_variant ; 3150.0bp to feature; MODIFIER silent_mutation Average:90.653; most accessible tissue: Zhenshan97 panicle, score: 95.951 N N N N
vg0702957519 T -> C LOC_Os07g06100-LOC_Os07g06110 intergenic_region ; MODIFIER silent_mutation Average:90.653; most accessible tissue: Zhenshan97 panicle, score: 95.951 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)
vg0702957519 T C -0.04 -0.03 -0.03 -0.06 -0.06 -0.07

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0702957519 7.11E-07 7.70E-30 mr1137 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
vg0702957519 NA 8.18E-11 mr1137 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
vg0702957519 NA 4.31E-06 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
vg0702957519 NA 9.26E-06 mr1380 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
vg0702957519 NA 8.78E-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
vg0702957519 NA 9.36E-06 mr1576 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
vg0702957519 NA 7.31E-08 mr1617 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
vg0702957519 NA 2.31E-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
vg0702957519 NA 6.22E-07 mr1955 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
vg0702957519 3.01E-06 3.01E-06 mr1955 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
vg0702957519 NA 1.25E-06 mr1977 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
vg0702957519 1.05E-08 6.89E-35 mr1137_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
vg0702957519 NA 7.84E-12 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
vg0702957519 2.41E-06 NA mr1138_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
vg0702957519 NA 4.83E-07 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
vg0702957519 3.87E-07 NA mr1354_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
vg0702957519 1.33E-06 NA mr1585_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
vg0702957519 1.08E-06 NA mr1617_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
vg0702957519 NA 1.94E-08 mr1617_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
vg0702957519 NA 8.14E-06 mr1840_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
vg0702957519 NA 1.73E-07 mr1880_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