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Detailed information for vg0422652665:

Variant ID: vg0422652665 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 22652665
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTTCTGCAATCGGCATGAAATCTGAACCAATCTCTGTTATGGAAGTATACTCTCAGCTGTTAAATTTTGAGAACAGACTTCAGCTCAAACAGGAAGGGAT[C/T]
GCTGCTGCCCATGCAGCGAGTCGCGGCCGCGGTGGGTTTATCCCACGCAGCGGCGGCAATGGTGGTGGCAGCGGCGGCTCTGGGCGTGGTCGTAGTGCAC

Reverse complement sequence

GTGCACTACGACCACGCCCAGAGCCGCCGCTGCCACCACCATTGCCGCCGCTGCGTGGGATAAACCCACCGCGGCCGCGACTCGCTGCATGGGCAGCAGC[G/A]
ATCCCTTCCTGTTTGAGCTGAAGTCTGTTCTCAAAATTTAACAGCTGAGAGTATACTTCCATAACAGAGATTGGTTCAGATTTCATGCCGATTGCAGAAA

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 89.60% 6.20% 4.17% 0.00% NA
All Indica  2759 82.90% 10.40% 6.78% 0.00% NA
All Japonica  1512 99.50% 0.00% 0.46% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 84.00% 1.70% 14.29% 0.00% NA
Indica II  465 45.20% 42.80% 12.04% 0.00% NA
Indica III  913 99.90% 0.00% 0.11% 0.00% NA
Indica Intermediate  786 84.50% 9.80% 5.73% 0.00% NA
Temperate Japonica  767 99.60% 0.00% 0.39% 0.00% NA
Tropical Japonica  504 99.80% 0.00% 0.20% 0.00% NA
Japonica Intermediate  241 98.80% 0.00% 1.24% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 87.80% 8.90% 3.33% 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
vg0422652665 C -> T LOC_Os04g38060.1 synonymous_variant ; p.Ile368Ile; LOW synonymous_codon Average:57.413; most accessible tissue: Zhenshan97 panicle, score: 73.605 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0422652665 NA 1.01E-06 mr1536 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
vg0422652665 NA 7.73E-06 mr1278_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
vg0422652665 NA 2.44E-08 mr1327_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
vg0422652665 NA 1.12E-07 mr1428_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
vg0422652665 NA 1.48E-06 mr1428_2 Ind_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
vg0422652665 NA 3.05E-06 mr1454_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