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Detailed information for vg0605170851:

Variant ID: vg0605170851 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 5170851
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.88, T: 0.12, others allele: 0.00, population size: 99. )

Flanking Sequence (100 bp) in Reference Genome:

ATGGAGCGGGTACTGCCAAAGTGAGGTTATTGAAAGGCTTTGTCGTGGCAAGTCTCATTCGTTGGGACGTAGGCTTATGTGTTGGGCAAGTCGCGGAGTA[T/C]
GGGTAAAGTGTACATCCACTACAGTATGAGTAAACCAATCTATTCGAATAGCCGTGCTCGCGGATATTGAGCACCGAGATATGTATTACACTTGGCTAGA

Reverse complement sequence

TCTAGCCAAGTGTAATACATATCTCGGTGCTCAATATCCGCGAGCACGGCTATTCGAATAGATTGGTTTACTCATACTGTAGTGGATGTACACTTTACCC[A/G]
TACTCCGCGACTTGCCCAACACATAAGCCTACGTCCCAACGAATGAGACTTGCCACGACAAAGCCTTTCAATAACCTCACTTTGGCAGTACCCGCTCCAT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	63.70%	34.70%	0.61%	0.97%	NA
All Indica	2759	70.90%	26.80%	0.62%	1.67%	NA
All Japonica	1512	46.20%	53.40%	0.40%	0.00%	NA
Aus	269	74.70%	24.20%	1.12%	0.00%	NA
Indica I	595	57.30%	41.20%	0.50%	1.01%	NA
Indica II	465	92.30%	6.00%	0.22%	1.51%	NA
Indica III	913	68.60%	27.80%	0.77%	2.85%	NA
Indica Intermediate	786	71.40%	27.00%	0.76%	0.89%	NA
Temperate Japonica	767	48.90%	50.80%	0.26%	0.00%	NA
Tropical Japonica	504	40.90%	58.70%	0.40%	0.00%	NA
Japonica Intermediate	241	48.50%	50.60%	0.83%	0.00%	NA
VI/Aromatic	96	99.00%	0.00%	1.04%	0.00%	NA
Intermediate	90	65.60%	32.20%	2.22%	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
vg0605170851	T -> C	LOC_Os06g10109-LOC_Os06g10130	intergenic_region ; MODIFIER	silent_mutation	Average:52.25; most accessible tissue: Zhenshan97 panicle, score: 85.665	N	N	N	N
vg0605170851	T -> DEL	N	N	silent_mutation	Average:52.25; most accessible tissue: Zhenshan97 panicle, score: 85.665	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0605170851	NA	7.11E-10	mr1201	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
vg0605170851	4.07E-09	9.66E-19	mr1201	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
vg0605170851	NA	1.48E-08	mr1219	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
vg0605170851	5.61E-07	4.12E-16	mr1219	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
vg0605170851	NA	1.50E-06	mr1236	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
vg0605170851	NA	7.00E-11	mr1274	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
vg0605170851	3.11E-09	3.86E-19	mr1274	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
vg0605170851	9.64E-07	8.96E-10	mr1201_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
vg0605170851	1.16E-09	2.46E-17	mr1201_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
vg0605170851	NA	4.82E-08	mr1219_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
vg0605170851	7.81E-09	9.22E-16	mr1219_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
vg0605170851	9.53E-06	9.85E-11	mr1274_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
vg0605170851	1.11E-07	1.81E-17	mr1274_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