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Detailed information for vg1125546169:

Variant ID: vg1125546169 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 25546169
Reference Allele: CAlternative Allele: G
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.94, C: 0.06, others allele: 0.00, population size: 94. )

Flanking Sequence (100 bp) in Reference Genome:


AACATCGGTACTTTCACGTGCAGACGTTACAACCACACGTGAAAACCTATTTCGTAGGTAGACTTTCTAAGGAGGCCGCTTGTAAAAACCAATTTTTTAA[C/G]
CGGCCAAGGCTAGACTGCAATGATTTTTTTCAAAAAGAAAGGACAAATCCAAAACCCTAACCAGGATCGCCGTGAGGCCGTCGACATCACGTGGTCGAGG

Reverse complement sequence

CCTCGACCACGTGATGTCGACGGCCTCACGGCGATCCTGGTTAGGGTTTTGGATTTGTCCTTTCTTTTTGAAAAAAATCATTGCAGTCTAGCCTTGGCCG[G/C]
TTAAAAAATTGGTTTTTACAAGCGGCCTCCTTAGAAAGTCTACCTACGAAATAGGTTTTCACGTGTGGTTGTAACGTCTGCACGTGAAAGTACCGATGTT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 57.40% 42.30% 0.36% 0.00% NA
All Indica  2759 55.40% 44.40% 0.14% 0.00% NA
All Japonica  1512 65.70% 33.50% 0.73% 0.00% NA
Aus  269 50.90% 48.70% 0.37% 0.00% NA
Indica I  595 16.00% 83.90% 0.17% 0.00% NA
Indica II  465 24.70% 75.30% 0.00% 0.00% NA
Indica III  913 91.60% 8.20% 0.22% 0.00% NA
Indica Intermediate  786 61.50% 38.40% 0.13% 0.00% NA
Temperate Japonica  767 51.50% 48.50% 0.00% 0.00% NA
Tropical Japonica  504 90.50% 8.90% 0.60% 0.00% NA
Japonica Intermediate  241 59.30% 37.30% 3.32% 0.00% NA
VI/Aromatic  96 1.00% 99.00% 0.00% 0.00% NA
Intermediate  90 55.60% 43.30% 1.11% 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
vg1125546169 C -> G LOC_Os11g42440.1 intron_variant ; MODIFIER silent_mutation Average:61.816; most accessible tissue: Minghui63 panicle, score: 84.005 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1125546169 NA 8.76E-10 Heading_date Ind_All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg1125546169 NA 6.31E-10 mr1063 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
vg1125546169 2.62E-13 1.36E-26 mr1133 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
vg1125546169 NA 2.94E-06 mr1533 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
vg1125546169 1.44E-06 1.44E-06 mr1540 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
vg1125546169 6.67E-08 2.22E-14 mr1662 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
vg1125546169 1.19E-08 8.47E-13 mr1662 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
vg1125546169 8.55E-06 NA mr1667 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
vg1125546169 7.77E-09 8.00E-15 mr1667 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
vg1125546169 8.12E-06 1.80E-06 mr1732 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
vg1125546169 NA 5.11E-07 mr1870 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
vg1125546169 NA 4.67E-07 mr1980 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
vg1125546169 NA 2.61E-07 mr1063_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
vg1125546169 1.73E-12 9.13E-26 mr1133_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
vg1125546169 NA 2.28E-06 mr1242_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
vg1125546169 1.59E-09 1.25E-17 mr1662_2 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
vg1125546169 3.42E-07 6.90E-11 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
vg1125546169 1.08E-09 2.00E-16 mr1667_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