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Detailed information for vg0137881863:

Variant ID: vg0137881863 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 37881863
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.75, T: 0.24, others allele: 0.00, population size: 313. )

Flanking Sequence (100 bp) in Reference Genome:


CCCAGTCGGCATCCGAGTAAGCGGTGAGCTCGTGTGGCGACGAAGCCGACAGAAGTATGCCGTGACAAAGTGTACCTTCGATATAGCGAAGAACTCGCTT[C/T]
ACCAGGTTCAAGTGACCTTCACGTGGATCATGCATGTGTAGACATATTTGTTGTACTGCATATGCTATGTCTGGCCTTGTGAATGTCAGATATTGGAGAG

Reverse complement sequence

CTCTCCAATATCTGACATTCACAAGGCCAGACATAGCATATGCAGTACAACAAATATGTCTACACATGCATGATCCACGTGAAGGTCACTTGAACCTGGT[G/A]
AAGCGAGTTCTTCGCTATATCGAAGGTACACTTTGTCACGGCATACTTCTGTCGGCTTCGTCGCCACACGAGCTCACCGCTTACTCGGATGCCGACTGGG

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 76.60% 23.00% 0.02% 0.38% NA
All Indica  2759 67.50% 31.90% 0.04% 0.62% NA
All Japonica  1512 99.50% 0.50% 0.00% 0.00% NA
Aus  269 29.40% 70.30% 0.00% 0.37% NA
Indica I  595 63.70% 35.60% 0.00% 0.67% NA
Indica II  465 85.40% 13.50% 0.00% 1.08% NA
Indica III  913 54.80% 44.90% 0.00% 0.33% NA
Indica Intermediate  786 74.40% 24.80% 0.13% 0.64% NA
Temperate Japonica  767 99.60% 0.40% 0.00% 0.00% NA
Tropical Japonica  504 99.60% 0.40% 0.00% 0.00% NA
Japonica Intermediate  241 99.20% 0.80% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 86.70% 13.30% 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
vg0137881863 C -> T LOC_Os01g65290.1 synonymous_variant ; p.Val273Val; LOW synonymous_codon Average:64.053; most accessible tissue: Minghui63 flower, score: 84.277 N N N N
vg0137881863 C -> DEL LOC_Os01g65290.1 N frameshift_variant Average:64.053; most accessible tissue: Minghui63 flower, score: 84.277 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0137881863 NA 6.62E-07 mr1375 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
vg0137881863 4.70E-09 NA mr1517 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
vg0137881863 1.57E-15 2.22E-17 mr1517 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
vg0137881863 2.23E-08 NA mr1538 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
vg0137881863 2.73E-12 1.41E-13 mr1538 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
vg0137881863 NA 6.86E-06 mr1274_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
vg0137881863 4.97E-10 NA mr1517_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
vg0137881863 3.89E-16 1.97E-16 mr1517_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
vg0137881863 1.21E-07 NA mr1538_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
vg0137881863 2.49E-12 4.11E-16 mr1538_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