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Detailed information for vg0506884765:

Variant ID: vg0506884765 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 6884765
Reference Allele: A	Alternative Allele: T
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, T: 0.01, others allele: 0.00, population size: 122. )

Flanking Sequence (100 bp) in Reference Genome:

TGGTGGCGGATGAATTCCACCGGGCCATTGGCGAGAAGCGATGGTAAAACCCCTACAAGAGGAGCTCCACGGGCCAAGGGTGGAGGCGGTGGTCTAGAGA[A/T]
TTTTGTGCCAGTGGTTCTTGTTCTTTCTCTTGTTGCAATCTTACTCAACATTGTTGCAGCGACGAACAGTTGAGCCAGGAACAACCATATGGCTCCTGTT

Reverse complement sequence

AACAGGAGCCATATGGTTGTTCCTGGCTCAACTGTTCGTCGCTGCAACAATGTTGAGTAAGATTGCAACAAGAGAAAGAACAAGAACCACTGGCACAAAA[T/A]
TCTCTAGACCACCGCCTCCACCCTTGGCCCGTGGAGCTCCTCTTGTAGGGGTTTTACCATCGCTTCTCGCCAATGGCCCGGTGGAATTCATCCGCCACCA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	53.70%	46.10%	0.15%	0.06%	NA
All Indica	2759	29.70%	70.00%	0.22%	0.11%	NA
All Japonica	1512	97.80%	2.20%	0.00%	0.00%	NA
Aus	269	30.10%	69.90%	0.00%	0.00%	NA
Indica I	595	10.60%	89.10%	0.34%	0.00%	NA
Indica II	465	50.10%	49.90%	0.00%	0.00%	NA
Indica III	913	35.70%	63.90%	0.22%	0.22%	NA
Indica Intermediate	786	25.10%	74.60%	0.25%	0.13%	NA
Temperate Japonica	767	98.80%	1.20%	0.00%	0.00%	NA
Tropical Japonica	504	96.80%	3.20%	0.00%	0.00%	NA
Japonica Intermediate	241	96.70%	3.30%	0.00%	0.00%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	70.00%	28.90%	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
vg0506884765	A -> T	LOC_Os05g12040.1	missense_variant ; p.Phe38Ile; MODERATE	nonsynonymous_codon ; F38I	Average:58.421; most accessible tissue: Callus, score: 75.097	unknown	unknown	TOLERATED	0.47
vg0506884765	A -> DEL	LOC_Os05g12040.1	N	frameshift_variant	Average:58.421; most accessible tissue: Callus, score: 75.097	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0506884765	3.13E-16	NA	mr1039	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
vg0506884765	3.54E-15	1.26E-18	mr1039	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
vg0506884765	NA	3.56E-15	mr1593	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
vg0506884765	NA	3.60E-10	mr1904	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
vg0506884765	1.11E-19	NA	mr1039_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
vg0506884765	4.88E-18	3.44E-19	mr1039_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
vg0506884765	NA	6.05E-14	mr1593_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
vg0506884765	3.75E-06	NA	mr1632_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
vg0506884765	2.39E-07	2.14E-07	mr1632_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
vg0506884765	NA	4.12E-08	mr1645_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