Search for Variation information by Variation ID:

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

Detailed information for vg1005659155:

Variant ID: vg1005659155 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 5659155
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.94, G: 0.06, others allele: 0.00, population size: 204. )

Flanking Sequence (100 bp) in Reference Genome:


CTTCGCTTTTGTCATGGAGAAAGTACACCTAAGTGAAGCGTGAAAAATCATCAACAATGACGAAACCATACTTGTTACCTCCAATGCTTATGTAGGCCAC[A/G]
TGCCCAAATAAATCCATATGAAGAAGCTCGAGTGGTCTTGTTGTAGTCATGATATTTTTTATAGGATGTGGACTCCCAACTTGCTTCCCGGCTTGGCAAG

Reverse complement sequence

CTTGCCAAGCCGGGAAGCAAGTTGGGAGTCCACATCCTATAAAAAATATCATGACTACAACAAGACCACTCGAGCTTCTTCATATGGATTTATTTGGGCA[T/C]
GTGGCCTACATAAGCATTGGAGGTAACAAGTATGGTTTCGTCATTGTTGATGATTTTTCACGCTTCACTTAGGTGTACTTTCTCCATGACAAAAGCGAAG

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 80.00% 19.60% 0.47% 0.00% NA
All Indica  2759 73.50% 25.70% 0.80% 0.00% NA
All Japonica  1512 89.60% 10.40% 0.00% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 91.10% 8.90% 0.00% 0.00% NA
Indica II  465 71.20% 27.30% 1.51% 0.00% NA
Indica III  913 69.40% 29.60% 0.99% 0.00% NA
Indica Intermediate  786 66.40% 32.80% 0.76% 0.00% NA
Temperate Japonica  767 87.50% 12.50% 0.00% 0.00% NA
Tropical Japonica  504 92.30% 7.70% 0.00% 0.00% NA
Japonica Intermediate  241 90.90% 9.10% 0.00% 0.00% NA
VI/Aromatic  96 58.30% 41.70% 0.00% 0.00% NA
Intermediate  90 80.00% 20.00% 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
vg1005659155 A -> G LOC_Os10g10300.1 synonymous_variant ; p.His708His; LOW synonymous_codon Average:37.344; most accessible tissue: Minghui63 flag leaf, score: 56.489 N N N N
vg1005659155 A -> G LOC_Os10g10300.1 synonymous_variant ; p.His708His; LOW nonsynonymous_codon ; H708P Average:37.344; most accessible tissue: Minghui63 flag leaf, score: 56.489 probably damaging -3.205 TOLERATED 1.00

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1005659155 NA 5.79E-07 mr1027_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
vg1005659155 NA 6.92E-07 mr1580_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
vg1005659155 NA 9.36E-06 mr1662_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
vg1005659155 NA 3.01E-06 mr1745_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
vg1005659155 NA 9.64E-09 mr1825_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
vg1005659155 NA 4.31E-06 mr1915_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
vg1005659155 1.85E-06 1.85E-06 mr1940_2 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
vg1005659155 NA 2.91E-07 mr1943_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