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Detailed information for vg0518676551:

Variant ID: vg0518676551 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 18676551
Reference Allele: CAlternative Allele: G,A
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 286. )

Flanking Sequence (100 bp) in Reference Genome:


GCCCTTGGTGAAGGCGGCGATGATGACGTCGTCGGTGATGTCAGAGATCTTGTTGCGTTGCTCGGAAAAGCGTCGGATGTAATCTCGAAGGGATTCTCCA[C/G,A]
ACTTCTGAACAACGTTGTAAAGATCAAACTGTGTACCAGGGCGTTCAAAGGTACCCTAGAAGTTGGCGATGAAGTGGTCGCGAAGTTCCACCCAAGATCC

Reverse complement sequence

GGATCTTGGGTGGAACTTCGCGACCACTTCATCGCCAACTTCTAGGGTACCTTTGAACGCCCTGGTACACAGTTTGATCTTTACAACGTTGTTCAGAAGT[G/C,T]
TGGAGAATCCCTTCGAGATTACATCCGACGCTTTTCCGAGCAACGCAACAAGATCTCTGACATCACCGACGACGTCATCATCGCCGCCTTCACCAAGGGC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 67.70% 31.20% 0.74% 0.38% A: 0.02%
All Indica  2759 98.60% 1.30% 0.07% 0.00% NA
All Japonica  1512 9.80% 86.90% 2.05% 1.19% A: 0.07%
Aus  269 98.90% 1.10% 0.00% 0.00% NA
Indica I  595 99.70% 0.20% 0.17% 0.00% NA
Indica II  465 97.00% 2.80% 0.22% 0.00% NA
Indica III  913 99.20% 0.80% 0.00% 0.00% NA
Indica Intermediate  786 98.10% 1.90% 0.00% 0.00% NA
Temperate Japonica  767 14.90% 79.30% 3.52% 2.22% A: 0.13%
Tropical Japonica  504 5.00% 94.80% 0.20% 0.00% NA
Japonica Intermediate  241 3.70% 94.60% 1.24% 0.41% NA
VI/Aromatic  96 9.40% 90.60% 0.00% 0.00% NA
Intermediate  90 60.00% 37.80% 2.22% 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
vg0518676551 C -> DEL LOC_Os05g32050.1 N frameshift_variant Average:61.215; most accessible tissue: Minghui63 flag leaf, score: 84.028 N N N N
vg0518676551 C -> G LOC_Os05g32050.1 missense_variant ; p.Cys515Ser; MODERATE nonsynonymous_codon ; C515S Average:61.215; most accessible tissue: Minghui63 flag leaf, score: 84.028 unknown unknown TOLERATED 1.00
vg0518676551 C -> A LOC_Os05g32050.1 missense_variant ; p.Cys515Phe; MODERATE nonsynonymous_codon ; C515F Average:61.215; most accessible tissue: Minghui63 flag leaf, score: 84.028 unknown unknown DELETERIOUS 0.03

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0518676551 NA 3.65E-08 mr1162 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
vg0518676551 NA 1.06E-10 mr1281 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
vg0518676551 NA 5.93E-10 mr1342 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
vg0518676551 NA 1.40E-20 mr1541 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
vg0518676551 NA 1.28E-10 mr1630 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
vg0518676551 1.14E-07 NA mr1137_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
vg0518676551 NA 3.31E-16 mr1342_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
vg0518676551 NA 1.27E-09 mr1398_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
vg0518676551 NA 1.55E-10 mr1537_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
vg0518676551 NA 2.12E-08 mr1600_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
vg0518676551 1.08E-06 5.63E-29 mr1617_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
vg0518676551 NA 4.32E-06 mr1617_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
vg0518676551 NA 1.53E-13 mr1713_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
vg0518676551 NA 2.04E-07 mr1749_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
vg0518676551 NA 1.87E-07 mr1804_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
vg0518676551 NA 2.37E-18 mr1945_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