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Detailed information for vg0411807088:

Variant ID: vg0411807088 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 11807088
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.02, others allele: 0.00, population size: 117. )

Flanking Sequence (100 bp) in Reference Genome:


GAAGGCTTCCCACAAGACGCCGGTACTGTGTAGCATCCACTTCCTCCGTCGTGCTATCACGGCTCAGCTTCAGTCTCTCCTCCATTGGAGTGAGAGCTGG[G/A]
TTGCAATCGGTGAGCCTAGCCAGCTCAACGACGCGCTTGGCGTAGGCGGTCTGTCGAAGCGTGATCCCGGAGTCGTCCTGGTGCACCTCAATCCCCAGGT

Reverse complement sequence

ACCTGGGGATTGAGGTGCACCAGGACGACTCCGGGATCACGCTTCGACAGACCGCCTACGCCAAGCGCGTCGTTGAGCTGGCTAGGCTCACCGATTGCAA[C/T]
CCAGCTCTCACTCCAATGGAGGAGAGACTGAAGCTGAGCCGTGATAGCACGACGGAGGAAGTGGATGCTACACAGTACCGGCGTCTTGTGGGAAGCCTTC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 66.70% 33.00% 0.34% 0.00% NA
All Indica  2759 54.60% 44.80% 0.58% 0.00% NA
All Japonica  1512 99.10% 0.90% 0.00% 0.00% NA
Aus  269 0.40% 99.60% 0.00% 0.00% NA
Indica I  595 77.30% 22.70% 0.00% 0.00% NA
Indica II  465 48.40% 48.80% 2.80% 0.00% NA
Indica III  913 47.50% 52.40% 0.11% 0.00% NA
Indica Intermediate  786 49.20% 50.50% 0.25% 0.00% NA
Temperate Japonica  767 99.60% 0.40% 0.00% 0.00% NA
Tropical Japonica  504 98.80% 1.20% 0.00% 0.00% NA
Japonica Intermediate  241 98.30% 1.70% 0.00% 0.00% NA
VI/Aromatic  96 85.40% 14.60% 0.00% 0.00% NA
Intermediate  90 68.90% 31.10% 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
vg0411807088 G -> A LOC_Os04g20990.1 intron_variant ; MODIFIER silent_mutation Average:19.769; most accessible tissue: Zhenshan97 root, score: 30.989 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0411807088 NA 4.74E-06 mr1120 Ind_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
vg0411807088 NA 6.31E-06 mr1373 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
vg0411807088 4.34E-06 4.33E-06 mr1396 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
vg0411807088 NA 3.67E-06 mr1445 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
vg0411807088 NA 4.08E-12 mr1846 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
vg0411807088 NA 4.43E-06 mr1846 Ind_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
vg0411807088 NA 1.57E-21 mr1846_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
vg0411807088 NA 1.51E-10 mr1846_2 Ind_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