Search for Variation information by Variation ID:

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

Detailed information for vg0703431182:

Variant ID: vg0703431182 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 3431182
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.90, A: 0.09, others allele: 0.00, population size: 286. )

Flanking Sequence (100 bp) in Reference Genome:


AAAGGTCATGAGAAAACTCATTAGCTGCAGCAAGGATCAAATCCTTAGGAGGCAATTCAGCTATGAAACATGCGCTTTGATTAACTGACAGCTGACTCAC[G/A]
CATGATTCAATCTGATTCTTAACAGCCCCAGTCCCTATCTCAAACTCAAACTCATTGTTGCTTTCTAGCGTATATCTGTTTGTTTTGTCCTTCACCACCA

Reverse complement sequence

TGGTGGTGAAGGACAAAACAAACAGATATACGCTAGAAAGCAACAATGAGTTTGAGTTTGAGATAGGGACTGGGGCTGTTAAGAATCAGATTGAATCATG[C/T]
GTGAGTCAGCTGTCAGTTAATCAAAGCGCATGTTTCATAGCTGAATTGCCTCCTAAGGATTTGATCCTTGCTGCAGCTAATGAGTTTTCTCATGACCTTT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 56.00% 43.60% 0.02% 0.36% NA
All Indica  2759 35.90% 63.60% 0.00% 0.51% NA
All Japonica  1512 99.70% 0.30% 0.00% 0.00% NA
Aus  269 3.30% 96.70% 0.00% 0.00% NA
Indica I  595 84.90% 14.80% 0.00% 0.34% NA
Indica II  465 15.10% 84.30% 0.00% 0.65% NA
Indica III  913 15.90% 83.70% 0.00% 0.44% NA
Indica Intermediate  786 34.40% 65.00% 0.00% 0.64% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.20% 0.80% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 90.60% 9.40% 0.00% 0.00% NA
Intermediate  90 61.10% 34.40% 1.11% 3.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0703431182 G -> DEL LOC_Os07g06970.1 N frameshift_variant Average:52.148; most accessible tissue: Callus, score: 88.688 N N N N
vg0703431182 G -> A LOC_Os07g06970.1 synonymous_variant ; p.Cys611Cys; LOW synonymous_codon Average:52.148; most accessible tissue: Callus, score: 88.688 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0703431182 NA 4.88E-06 mr1130 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
vg0703431182 NA 4.17E-07 mr1291 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
vg0703431182 NA 6.64E-06 mr1496 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
vg0703431182 NA 6.15E-06 mr1531 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
vg0703431182 NA 2.66E-17 mr1557 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
vg0703431182 NA 9.32E-06 mr1679 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
vg0703431182 NA 6.24E-06 mr1904 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
vg0703431182 NA 8.66E-08 mr1170_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