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Detailed information for vg0400052458:

Variant ID: vg0400052458 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 52458
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.89, C: 0.09, others allele: 0.00, population size: 45. )

Flanking Sequence (100 bp) in Reference Genome:

TGCCGTGTAATCCATGCATTGGACTTACCGATGTTCCTGGCGCGAACTACAGCCAAGTGCTCCTCGATGTAAGGAGCTACCAATGAAGAGTGTTGCAGAA[T/C]
AGTGAAATGGGCTTTACAGAATAAATTGTTGTCTACCATCATTATTGCTTTCCTTCCTAGAGTTCCCTTTCCCCGTAGTCTCCCTTCATGGCGTGATTCA

Reverse complement sequence

TGAATCACGCCATGAAGGGAGACTACGGGGAAAGGGAACTCTAGGAAGGAAAGCAATAATGATGGTAGACAACAATTTATTCTGTAAAGCCCATTTCACT[A/G]
TTCTGCAACACTCTTCATTGGTAGCTCCTTACATCGAGGAGCACTTGGCTGTAGTTCGCGCCAGGAACATCGGTAAGTCCAATGCATGGATTACACGGCA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	58.00%	19.50%	6.01%	16.46%	NA
All Indica	2759	93.20%	2.10%	1.88%	2.79%	NA
All Japonica	1512	5.80%	55.50%	3.57%	35.19%	NA
Aus	269	9.70%	1.50%	57.62%	31.23%	NA
Indica I	595	96.30%	2.50%	0.67%	0.50%	NA
Indica II	465	95.50%	2.20%	1.08%	1.29%	NA
Indica III	913	95.40%	1.40%	1.64%	1.53%	NA
Indica Intermediate	786	87.00%	2.50%	3.56%	6.87%	NA
Temperate Japonica	767	1.80%	87.40%	0.26%	10.56%	NA
Tropical Japonica	504	10.70%	16.30%	9.33%	63.69%	NA
Japonica Intermediate	241	7.90%	36.10%	2.07%	53.94%	NA
VI/Aromatic	96	8.30%	1.00%	13.54%	77.08%	NA
Intermediate	90	54.40%	22.20%	11.11%	12.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0400052458	T -> C	LOC_Os04g01060.1	missense_variant ; p.Ile705Val; MODERATE	nonsynonymous_codon ; I705V	Average:13.418; most accessible tissue: Callus, score: 27.12	benign	-0.408	TOLERATED	1.00
vg0400052458	T -> DEL	LOC_Os04g01060.1	N	frameshift_variant	Average:13.418; most accessible tissue: Callus, score: 27.12	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0400052458	1.95E-06	NA	mr1059	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
vg0400052458	NA	4.23E-06	mr1082	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
vg0400052458	NA	4.50E-06	mr1543	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
vg0400052458	NA	1.05E-09	mr1769	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
vg0400052458	NA	2.72E-06	mr1011_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
vg0400052458	NA	6.85E-07	mr1252_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
vg0400052458	NA	1.19E-06	mr1252_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
vg0400052458	NA	7.81E-07	mr1263_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
vg0400052458	NA	1.74E-06	mr1550_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
vg0400052458	NA	1.38E-08	mr1563_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
vg0400052458	NA	2.60E-09	mr1769_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
vg0400052458	NA	3.51E-07	mr1780_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
vg0400052458	NA	1.51E-08	mr1871_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