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Detailed information for vg0715863395:

Variant ID: vg0715863395 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 15863395
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TAGTACTAGTTCCCAAGATTACAGCGCAAACATTTCCAGTTTCTTTCTATATTGACGATCATCCTTTTTTTTTCTCCCATCTCTTGCAATCGATTATCCT[T/C]
CCGCCATCACCTCTCTCTTTTTTTTTGGCGTTTGCCTGTTCGGCAAGAGATATTAGTAATACACACTTAGAGCCTATTTGATTCCCCTATCAAAATTTTA

Reverse complement sequence

TAAAATTTTGATAGGGGAATCAAATAGGCTCTAAGTGTGTATTACTAATATCTCTTGCCGAACAGGCAAACGCCAAAAAAAAAGAGAGAGGTGATGGCGG[A/G]
AGGATAATCGATTGCAAGAGATGGGAGAAAAAAAAAGGATGATCGTCAATATAGAAAGAAACTGGAAATGTTTGCGCTGTAATCTTGGGAACTAGTACTA

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 93.00% 6.10% 0.87% 0.00% NA
All Indica  2759 99.20% 0.50% 0.29% 0.00% NA
All Japonica  1512 80.50% 17.80% 1.72% 0.00% NA
Aus  269 97.40% 0.00% 2.60% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 97.60% 2.20% 0.22% 0.00% NA
Indica III  913 99.80% 0.10% 0.11% 0.00% NA
Indica Intermediate  786 98.70% 0.50% 0.76% 0.00% NA
Temperate Japonica  767 64.00% 32.70% 3.26% 0.00% NA
Tropical Japonica  504 99.40% 0.60% 0.00% 0.00% NA
Japonica Intermediate  241 93.40% 6.20% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 93.30% 6.70% 0.00% 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
vg0715863395 T -> C LOC_Os07g27290.1 downstream_gene_variant ; 424.0bp to feature; MODIFIER silent_mutation Average:36.932; most accessible tissue: Zhenshan97 root, score: 59.664 N N N N
vg0715863395 T -> C LOC_Os07g27290-LOC_Os07g27300 intergenic_region ; MODIFIER silent_mutation Average:36.932; most accessible tissue: Zhenshan97 root, score: 59.664 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0715863395 NA 3.45E-06 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
vg0715863395 NA 9.16E-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
vg0715863395 NA 5.43E-06 mr1902 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
vg0715863395 NA 3.06E-06 mr1011_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
vg0715863395 1.40E-06 2.98E-06 mr1321_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
vg0715863395 NA 3.06E-07 mr1588_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
vg0715863395 NA 5.25E-08 mr1709_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