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Detailed information for vg0819589271:

Variant ID: vg0819589271 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 19589271
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTCTTTTTTTTTTCACTATGAACACACGCACGTAAACCCTACCTATGAGCATCTTCGAAAACTAGGCCGATAAATCCTGAAGAGATTGACGAAGTCACCA[T/C]
AGGCGTCTCGCTGTCGACGGGCACGTCGCCTACCACTGAAAGCACAATGCCGTTAAATCGCCTACCACTGAAAGCACAACACCGTTAAATCCTGAAAAAT

Reverse complement sequence

ATTTTTCAGGATTTAACGGTGTTGTGCTTTCAGTGGTAGGCGATTTAACGGCATTGTGCTTTCAGTGGTAGGCGACGTGCCCGTCGACAGCGAGACGCCT[A/G]
TGGTGACTTCGTCAATCTCTTCAGGATTTATCGGCCTAGTTTTCGAAGATGCTCATAGGTAGGGTTTACGTGCGTGTGTTCATAGTGAAAAAAAAAAGAA

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 65.10% 34.20% 0.13% 0.55% NA
All Indica  2759 94.70% 5.10% 0.07% 0.14% NA
All Japonica  1512 26.10% 73.90% 0.00% 0.00% NA
Aus  269 12.30% 78.80% 1.12% 7.81% NA
Indica I  595 98.00% 1.80% 0.17% 0.00% NA
Indica II  465 95.10% 4.70% 0.22% 0.00% NA
Indica III  913 95.40% 4.60% 0.00% 0.00% NA
Indica Intermediate  786 91.10% 8.40% 0.00% 0.51% NA
Temperate Japonica  767 17.50% 82.50% 0.00% 0.00% NA
Tropical Japonica  504 24.20% 75.80% 0.00% 0.00% NA
Japonica Intermediate  241 57.30% 42.70% 0.00% 0.00% NA
VI/Aromatic  96 3.10% 95.80% 1.04% 0.00% NA
Intermediate  90 40.00% 58.90% 0.00% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0819589271 T -> C LOC_Os08g31630-LOC_Os08g31649 intergenic_region ; MODIFIER silent_mutation Average:51.693; most accessible tissue: Zhenshan97 flag leaf, score: 70.007 N N N N
vg0819589271 T -> DEL N N silent_mutation Average:51.693; most accessible tissue: Zhenshan97 flag leaf, score: 70.007 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0819589271 6.68E-07 NA mr1089 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
vg0819589271 NA 5.26E-07 mr1123 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
vg0819589271 NA 6.79E-07 mr1220 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
vg0819589271 NA 2.08E-06 mr1240 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
vg0819589271 NA 1.15E-06 mr1117_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
vg0819589271 NA 4.71E-06 mr1119_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
vg0819589271 NA 2.40E-06 mr1123_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
vg0819589271 NA 3.42E-07 mr1240_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
vg0819589271 NA 2.50E-06 mr1496_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