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Detailed information for vg1218287578:

Variant ID: vg1218287578 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 18287578
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.81, T: 0.18, others allele: 0.00, population size: 186. )

Flanking Sequence (100 bp) in Reference Genome:


AGCAAATGCTACTCATTATAAGGATTTCGACAAAGCAAATTTGTTCATCACTAAAGCCGAAGTCAATAGGAGTACTATTATGAATAAATTCAGACCTCAG[G/T]
CTCGAGGACGTAGTTCTCCCATAAATAAAACCATGTGTCATATAACAATTCTACTAAATATAGTAAGAGCATAGTTGAAAATGGTATTCGGTGCACTTTC

Reverse complement sequence

GAAAGTGCACCGAATACCATTTTCAACTATGCTCTTACTATATTTAGTAGAATTGTTATATGACACATGGTTTTATTTATGGGAGAACTACGTCCTCGAG[C/A]
CTGAGGTCTGAATTTATTCATAATAGTACTCCTATTGACTTCGGCTTTAGTGATGAACAAATTTGCTTTGTCGAAATCCTTATAATGAGTAGCATTTGCT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 60.90% 38.40% 0.13% 0.59% NA
All Indica  2759 40.80% 58.30% 0.07% 0.76% NA
All Japonica  1512 99.00% 0.70% 0.07% 0.20% NA
Aus  269 36.80% 62.80% 0.00% 0.37% NA
Indica I  595 57.50% 41.70% 0.17% 0.67% NA
Indica II  465 31.40% 67.70% 0.00% 0.86% NA
Indica III  913 36.70% 62.50% 0.00% 0.77% NA
Indica Intermediate  786 38.70% 60.40% 0.13% 0.76% NA
Temperate Japonica  767 99.20% 0.70% 0.13% 0.00% NA
Tropical Japonica  504 99.40% 0.20% 0.00% 0.40% NA
Japonica Intermediate  241 97.50% 2.10% 0.00% 0.41% NA
VI/Aromatic  96 93.80% 5.20% 1.04% 0.00% NA
Intermediate  90 73.30% 21.10% 2.22% 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
vg1218287578 G -> DEL LOC_Os12g30460.1 N frameshift_variant Average:32.315; most accessible tissue: Zhenshan97 young leaf, score: 53.969 N N N N
vg1218287578 G -> T LOC_Os12g30460.1 missense_variant ; p.Pro106Thr; MODERATE nonsynonymous_codon ; P106T Average:32.315; most accessible tissue: Zhenshan97 young leaf, score: 53.969 unknown unknown TOLERATED 0.26

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1218287578 NA 2.40E-07 mr1013 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
vg1218287578 NA 3.59E-06 mr1014 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
vg1218287578 NA 1.34E-09 mr1031 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
vg1218287578 NA 5.68E-07 mr1034 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
vg1218287578 NA 4.23E-09 mr1056 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
vg1218287578 NA 6.32E-06 mr1098 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
vg1218287578 NA 1.17E-06 mr1398 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
vg1218287578 NA 9.35E-08 mr1559 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
vg1218287578 NA 9.99E-06 mr1631 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
vg1218287578 NA 2.30E-07 mr1761 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
vg1218287578 NA 3.58E-06 mr1817 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
vg1218287578 NA 6.05E-06 mr1918 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
vg1218287578 NA 2.58E-06 mr1031_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
vg1218287578 NA 8.75E-07 mr1359_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
vg1218287578 NA 8.18E-10 mr1739_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