\

Search for Variation information by Variation ID:

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

Detailed information for vg0507885416:

Variant ID: vg0507885416 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 7885416
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, T: 0.03, others allele: 0.00, population size: 115. )

Flanking Sequence (100 bp) in Reference Genome:


TCGGAAGAACGGCACTCACGAAGTTCATGGCCGCATCTTACTACGTGTATCAGGTACTCAAGATGCCCGGGCCGAATGAAACAATCACTATCCAAGGGAA[C/T]
GCAAAGCTAGCGGTCCAATGCGACAAGCGGAGCCTCGACATGGTCGAGCACACTCCCAGCCCACCCGCCACAGCCGAGCCACCCAAGAAAGTGATCAAAA

Reverse complement sequence

TTTTGATCACTTTCTTGGGTGGCTCGGCTGTGGCGGGTGGGCTGGGAGTGTGCTCGACCATGTCGAGGCTCCGCTTGTCGCATTGGACCGCTAGCTTTGC[G/A]
TTCCCTTGGATAGTGATTGTTTCATTCGGCCCGGGCATCTTGAGTACCTGATACACGTAGTAAGATGCGGCCATGAACTTCGTGAGTGCCGTTCTTCCGA

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 51.70% 47.90% 0.32% 0.00% NA
All Indica  2759 21.10% 78.40% 0.51% 0.00% NA
All Japonica  1512 98.80% 1.20% 0.00% 0.00% NA
Aus  269 78.40% 21.20% 0.37% 0.00% NA
Indica I  595 4.50% 95.30% 0.17% 0.00% NA
Indica II  465 32.70% 67.30% 0.00% 0.00% NA
Indica III  913 24.50% 74.30% 1.20% 0.00% NA
Indica Intermediate  786 22.90% 76.80% 0.25% 0.00% NA
Temperate Japonica  767 98.20% 1.80% 0.00% 0.00% NA
Tropical Japonica  504 99.40% 0.60% 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 67.80% 32.20% 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
vg0507885416 C -> T LOC_Os05g14110.1 synonymous_variant ; p.Asn794Asn; LOW synonymous_codon Average:31.645; most accessible tissue: Zhenshan97 flag leaf, score: 44.637 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0507885416 7.20E-07 1.25E-30 mr1039 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
vg0507885416 NA 1.43E-08 mr1039 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
vg0507885416 5.08E-06 3.12E-28 mr1632 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
vg0507885416 NA 4.34E-08 mr1632 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
vg0507885416 1.23E-09 2.76E-33 mr1039_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
vg0507885416 1.70E-07 2.65E-08 mr1039_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
vg0507885416 NA 2.35E-15 mr1514_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
vg0507885416 5.78E-10 2.62E-34 mr1632_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
vg0507885416 4.13E-08 3.86E-09 mr1632_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