\

Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0509823730:

Variant ID: vg0509823730 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 9823730
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GAGTCTGACCTCCCACTTTTTCAAGCACAACCAATCCCGTCGAAGCAAACTACTGGCTGCACGTGGTTAACAAGAAGTTGGACCTCATCCAATGTAATGA[T/C]
GAAGAGAAAGTCGCCTTCGCCGCTCACCAACTGCATGGACCTGCTTCCGAGTGGTGGGACCACTTCCAGGCCACCCAGCCAGCTGGACAAATTATTACTT

Reverse complement sequence

AAGTAATAATTTGTCCAGCTGGCTGGGTGGCCTGGAAGTGGTCCCACCACTCGGAAGCAGGTCCATGCAGTTGGTGAGCGGCGAAGGCGACTTTCTCTTC[A/G]
TCATTACATTGGATGAGGTCCAACTTCTTGTTAACCACGTGCAGCCAGTAGTTTGCTTCGACGGGATTGGTTGTGCTTGAAAAAGTGGGAGGTCAGACTC

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 91.80% 7.90% 0.30% 0.00% NA
All Indica  2759 92.40% 7.10% 0.47% 0.00% NA
All Japonica  1512 99.70% 0.30% 0.00% 0.00% NA
Aus  269 37.50% 62.10% 0.37% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.40% 0.40% 0.22% 0.00% NA
Indica III  913 82.70% 16.10% 1.20% 0.00% NA
Indica Intermediate  786 93.90% 6.00% 0.13% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.20% 0.80% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 92.20% 7.80% 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
vg0509823730 T -> C LOC_Os05g17150.1 intron_variant ; MODIFIER silent_mutation Average:47.612; most accessible tissue: Zhenshan97 young leaf, score: 80.848 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0509823730 NA 1.04E-06 mr1157 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
vg0509823730 7.18E-06 NA mr1131_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
vg0509823730 6.67E-07 NA mr1263_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
vg0509823730 5.90E-06 NA mr1304_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
vg0509823730 4.81E-06 NA mr1316_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
vg0509823730 2.26E-07 NA mr1386_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
vg0509823730 NA 1.54E-09 mr1818_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