Search for Variation information by Variation ID:

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

Detailed information for vg1104136577:

Variant ID: vg1104136577 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 4136577
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 340. )

Flanking Sequence (100 bp) in Reference Genome:


AGAACCAGCAGCAATGAGCTGGTCATCTGTTATTGTCAAGCATGTCAAGGGAGAAGAGTGAAGCCTGTATAACACAGTTAAATAGGCATCAGCTGCAGGA[C/A]
ATACTAATATAGAATGCAGAACTGTACATCACAGGGGCAAAATTGTCTCTTTTTTTCTGCATTTGTAATTATTAATCCTTCAAAAATTTCTTAAATATGT

Reverse complement sequence

ACATATTTAAGAAATTTTTGAAGGATTAATAATTACAAATGCAGAAAAAAAGAGACAATTTTGCCCCTGTGATGTACAGTTCTGCATTCTATATTAGTAT[G/T]
TCCTGCAGCTGATGCCTATTTAACTGTGTTATACAGGCTTCACTCTTCTCCCTTGACATGCTTGACAATAACAGATGACCAGCTCATTGCTGCTGGTTCT

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 88.20% 11.70% 0.02% 0.00% NA
All Indica  2759 95.00% 5.00% 0.00% 0.00% NA
All Japonica  1512 82.30% 17.60% 0.07% 0.00% NA
Aus  269 49.40% 50.60% 0.00% 0.00% NA
Indica I  595 81.80% 18.20% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 99.80% 0.20% 0.00% 0.00% NA
Indica Intermediate  786 96.60% 3.40% 0.00% 0.00% NA
Temperate Japonica  767 97.90% 2.10% 0.00% 0.00% NA
Tropical Japonica  504 55.80% 44.00% 0.20% 0.00% NA
Japonica Intermediate  241 88.40% 11.60% 0.00% 0.00% NA
VI/Aromatic  96 96.90% 3.10% 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
vg1104136577 C -> A LOC_Os11g07970.1 intron_variant ; MODIFIER silent_mutation Average:60.445; most accessible tissue: Callus, score: 74.609 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1104136577 NA 4.02E-06 mr1179 Jap_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
vg1104136577 1.61E-12 NA mr1638 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
vg1104136577 4.03E-07 1.34E-08 mr1638 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
vg1104136577 9.44E-06 NA mr1699 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
vg1104136577 NA 3.71E-06 mr1826 Jap_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
vg1104136577 NA 2.07E-07 mr1676_2 Jap_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