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Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0507368901:

Variant ID: vg0507368901 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 7368901
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.95, A: 0.04, others allele: 0.00, population size: 103. )

Flanking Sequence (100 bp) in Reference Genome:


AGTACATCACAAAACATAATCTATGGAATAAATTAGTAATGTTGTTGATAAATCCCAATGCAGGAAAAAAATATCCTTATATAATTTTAGATTTGTATAA[C/A]
AAATATTTTTTAAAAAATAACAGCCAAACACCACGGTATTAACTATTCAGTGCTTAAAAAGAAGAATCCAGGGTATTTTGTGATTTCTGGAAATTCCGAG

Reverse complement sequence

CTCGGAATTTCCAGAAATCACAAAATACCCTGGATTCTTCTTTTTAAGCACTGAATAGTTAATACCGTGGTGTTTGGCTGTTATTTTTTAAAAAATATTT[G/T]
TTATACAAATCTAAAATTATATAAGGATATTTTTTTCCTGCATTGGGATTTATCAACAACATTACTAATTTATTCCATAGATTATGTTTTGTGATGTACT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 49.80% 49.50% 0.68% 0.00% NA
All Indica  2759 21.70% 77.30% 0.98% 0.00% NA
All Japonica  1512 91.50% 8.20% 0.26% 0.00% NA
Aus  269 81.80% 17.80% 0.37% 0.00% NA
Indica I  595 3.00% 97.00% 0.00% 0.00% NA
Indica II  465 37.20% 60.20% 2.58% 0.00% NA
Indica III  913 25.40% 73.60% 0.99% 0.00% NA
Indica Intermediate  786 22.30% 77.00% 0.76% 0.00% NA
Temperate Japonica  767 98.30% 1.70% 0.00% 0.00% NA
Tropical Japonica  504 79.20% 20.20% 0.60% 0.00% NA
Japonica Intermediate  241 95.90% 3.70% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 61.10% 38.90% 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
vg0507368901 C -> A LOC_Os05g13300.1 intron_variant ; MODIFIER silent_mutation Average:29.389; most accessible tissue: Zhenshan97 panicle, score: 46.362 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0507368901 6.60E-06 NA mr1039 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
vg0507368901 3.76E-07 3.61E-13 mr1039 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
vg0507368901 NA 5.56E-13 mr1531 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
vg0507368901 9.29E-06 NA mr1593 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
vg0507368901 2.22E-06 3.51E-14 mr1593 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
vg0507368901 NA 2.88E-06 mr1632 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
vg0507368901 NA 6.22E-08 mr1860 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
vg0507368901 6.36E-07 3.22E-14 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
vg0507368901 9.78E-06 NA mr1593_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
vg0507368901 1.46E-07 1.31E-15 mr1593_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
vg0507368901 NA 4.20E-11 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
vg0507368901 NA 1.63E-06 mr1655_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