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Detailed information for vg0319641267:

Variant ID: vg0319641267 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 19641267
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATAGCTTTAAACGGGATCAACATACTCAAAGGGTTGTTTGGGATCTGTGTAACTTGCCTTGCTGGCCTTGGAACTCTTCAAATTCTTCTCTTGCAAAAAC[G/T]
GACTCTCCGGAAACGTCGGAATCTAAAGAGAAAAGAGCAAAATCACCAAAACAGCACATAAAAAAGCATGAACAGTACATGTGGATATTTTAACATGTAG

Reverse complement sequence

CTACATGTTAAAATATCCACATGTACTGTTCATGCTTTTTTATGTGCTGTTTTGGTGATTTTGCTCTTTTCTCTTTAGATTCCGACGTTTCCGGAGAGTC[C/A]
GTTTTTGCAAGAGAAGAATTTGAAGAGTTCCAAGGCCAGCAAGGCAAGTTACACAGATCCCAAACAACCCTTTGAGTATGTTGATCCCGTTTAAAGCTAT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 32.70% 0.40% 30.00% 36.90% NA
All Indica  2759 3.60% 0.50% 37.77% 58.10% NA
All Japonica  1512 86.00% 0.10% 11.44% 2.51% NA
Aus  269 10.40% 0.00% 63.20% 26.39% NA
Indica I  595 3.90% 0.00% 39.33% 56.81% NA
Indica II  465 4.30% 1.50% 29.25% 64.95% NA
Indica III  913 1.60% 0.00% 47.65% 50.71% NA
Indica Intermediate  786 5.20% 1.00% 30.15% 63.61% NA
Temperate Japonica  767 99.60% 0.00% 0.00% 0.39% NA
Tropical Japonica  504 66.50% 0.00% 31.35% 2.18% NA
Japonica Intermediate  241 83.40% 0.40% 6.22% 9.96% NA
VI/Aromatic  96 71.90% 0.00% 21.88% 6.25% NA
Intermediate  90 56.70% 1.10% 13.33% 28.89% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0319641267 G -> T LOC_Os03g35420.1 missense_variant ; p.Pro31Gln; MODERATE nonsynonymous_codon ; P31Q Average:7.841; most accessible tissue: Callus, score: 9.865 probably damaging 2.093 DELETERIOUS 0.00
vg0319641267 G -> DEL LOC_Os03g35420.1 N frameshift_variant Average:7.841; most accessible tissue: Callus, score: 9.865 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0319641267 NA 2.87E-16 mr1156 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
vg0319641267 NA 2.08E-10 mr1299 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
vg0319641267 NA 5.44E-06 mr1314 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
vg0319641267 NA 9.91E-06 mr1377 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
vg0319641267 4.63E-06 4.63E-06 mr1419 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
vg0319641267 NA 7.87E-06 mr1439 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
vg0319641267 NA 3.06E-08 mr1624 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
vg0319641267 NA 5.34E-10 mr1637 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
vg0319641267 NA 7.97E-10 mr1663 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
vg0319641267 7.81E-06 7.81E-06 mr1687 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
vg0319641267 NA 4.47E-16 mr1700 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
vg0319641267 NA 1.17E-11 mr1713 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
vg0319641267 NA 2.78E-06 mr1727 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
vg0319641267 NA 5.75E-08 mr1756 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
vg0319641267 9.02E-06 9.01E-06 mr1774 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
vg0319641267 NA 9.44E-07 mr1785 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
vg0319641267 NA 3.87E-08 mr1804 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
vg0319641267 NA 4.30E-06 mr1837 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
vg0319641267 NA 4.69E-07 mr1915 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
vg0319641267 NA 6.81E-06 mr1988 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