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Detailed information for vg0322560129:

Variant ID: vg0322560129 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 22560129
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 122. )

Flanking Sequence (100 bp) in Reference Genome:


TTACTGGCTCACTGTGTTGAAAGTATGTCTTGAGCAAATCAAGAAGTGCGAAAGTTGCCAGCGTCATGGCCGAAGCCAAACCGCGCCCCAGTATGAGTTG[C/T]
AGCCCATCGCACCAATTTGGCCATTCGCCAGATGGGGACTGGACATTATTGGGCCGTTCCCGGCGGCGCGAAACGGGCACAAGTTCACAATTGTGGCCGT

Reverse complement sequence

ACGGCCACAATTGTGAACTTGTGCCCGTTTCGCGCCGCCGGGAACGGCCCAATAATGTCCAGTCCCCATCTGGCGAATGGCCAAATTGGTGCGATGGGCT[G/A]
CAACTCATACTGGGGCGCGGTTTGGCTTCGGCCATGACGCTGGCAACTTTCGCACTTCTTGATTTGCTCAAGACATACTTTCAACACAGTGAGCCAGTAA

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 74.00% 25.30% 0.38% 0.30% NA
All Indica  2759 58.20% 40.60% 0.65% 0.51% NA
All Japonica  1512 99.70% 0.30% 0.00% 0.00% NA
Aus  269 78.80% 21.20% 0.00% 0.00% NA
Indica I  595 52.30% 47.10% 0.34% 0.34% NA
Indica II  465 80.40% 19.10% 0.22% 0.22% NA
Indica III  913 49.30% 48.80% 1.10% 0.77% NA
Indica Intermediate  786 59.90% 38.90% 0.64% 0.51% NA
Temperate Japonica  767 99.70% 0.30% 0.00% 0.00% NA
Tropical Japonica  504 99.60% 0.40% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 87.80% 12.20% 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
vg0322560129 C -> T LOC_Os03g40570.1 stop_gained ; p.Gln62*; HIGH stop_gained Average:49.695; most accessible tissue: Zhenshan97 panicle, score: 63.607 N N N N
vg0322560129 C -> DEL LOC_Os03g40570.1 N frameshift_variant Average:49.695; most accessible tissue: Zhenshan97 panicle, score: 63.607 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0322560129 NA 5.15E-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
vg0322560129 NA 7.90E-07 mr1045_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
vg0322560129 NA 7.26E-06 mr1204_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
vg0322560129 NA 1.62E-06 mr1250_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
vg0322560129 NA 1.15E-07 mr1408_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
vg0322560129 NA 3.78E-06 mr1528_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
vg0322560129 NA 4.00E-06 mr1566_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
vg0322560129 NA 2.95E-07 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
vg0322560129 NA 1.46E-09 mr1739_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
vg0322560129 NA 2.56E-07 mr1785_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
vg0322560129 NA 1.94E-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
vg0322560129 NA 6.31E-09 mr1837_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
vg0322560129 8.90E-07 NA mr1873_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
vg0322560129 NA 1.32E-07 mr1873_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
vg0322560129 NA 1.04E-06 mr1876_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