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Detailed information for vg0727503955:

Variant ID: vg0727503955 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 27503955
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 88. )

Flanking Sequence (100 bp) in Reference Genome:


TACTTAGGCCGAGTTTAGTTCTAAATTTTTTCTTCAAACTTTCAACTTTTTCATCACATCAAAACTTTCCTACACACACAAACTTCCAACTTTTTCATCA[C/T]
ATCGTTCCAATTTCAACCAAACTTCCAATTTTGACGTGAACTGAACACACCCTTCCAATTTTGTATTATTTTTTACAACAAATTGGCTAGTCTTGAATTG

Reverse complement sequence

CAATTCAAGACTAGCCAATTTGTTGTAAAAAATAATACAAAATTGGAAGGGTGTGTTCAGTTCACGTCAAAATTGGAAGTTTGGTTGAAATTGGAACGAT[G/A]
TGATGAAAAAGTTGGAAGTTTGTGTGTGTAGGAAAGTTTTGATGTGATGAAAAAGTTGAAAGTTTGAAGAAAAAATTTAGAACTAAACTCGGCCTAAGTA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 32.50% 21.40% 1.10% 44.96% NA
All Indica  2759 25.10% 7.10% 1.45% 66.36% NA
All Japonica  1512 45.70% 52.90% 0.40% 0.99% NA
Aus  269 38.30% 1.50% 1.12% 59.11% NA
Indica I  595 7.90% 3.40% 1.68% 87.06% NA
Indica II  465 8.80% 1.70% 3.23% 86.24% NA
Indica III  913 50.20% 2.10% 0.88% 46.88% NA
Indica Intermediate  786 18.70% 18.80% 0.89% 61.58% NA
Temperate Japonica  767 65.60% 33.20% 0.13% 1.04% NA
Tropical Japonica  504 22.00% 77.00% 0.60% 0.40% NA
Japonica Intermediate  241 32.00% 65.10% 0.83% 2.07% NA
VI/Aromatic  96 10.40% 0.00% 1.04% 88.54% NA
Intermediate  90 44.40% 14.40% 2.22% 38.89% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0727503955 C -> DEL N N silent_mutation Average:12.976; most accessible tissue: Callus, score: 57.237 N N N N
vg0727503955 C -> T LOC_Os07g46080.1 intron_variant ; MODIFIER silent_mutation Average:12.976; most accessible tissue: Callus, score: 57.237 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0727503955 NA 1.15E-09 mr1002 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
vg0727503955 NA 2.51E-06 mr1200 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
vg0727503955 NA 1.21E-06 mr1705 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
vg0727503955 NA 4.66E-11 mr1002_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
vg0727503955 NA 2.85E-06 mr1186_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
vg0727503955 NA 3.12E-09 mr1369_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
vg0727503955 NA 7.48E-09 mr1453_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
vg0727503955 NA 2.83E-07 mr1616_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
vg0727503955 NA 3.99E-08 mr1652_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
vg0727503955 NA 3.59E-09 mr1851_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
vg0727503955 NA 8.83E-13 mr1864_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
vg0727503955 NA 4.20E-06 mr1992_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