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Detailed information for vg0825753695:

Variant ID: vg0825753695 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 25753695
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CCTGTCGCCGCCGCCGGTCTGACCGCAGGTCACCCGCCGGTCTGACCACCACGATGCCGCCGGTCTGACCGCCGGTGTGTCGCCGGTTAGACCACTGAAA[C/T]
CCGGTGAAACACAAATCGAATAACTCTTAAAGTGGATGATGACTTTATTACTTCTCTCTGTGTTTACAAAGTGCACCTACAGCACTCCTTACAAAATTTT

Reverse complement sequence

AAAATTTTGTAAGGAGTGCTGTAGGTGCACTTTGTAAACACAGAGAGAAGTAATAAAGTCATCATCCACTTTAAGAGTTATTCGATTTGTGTTTCACCGG[G/A]
TTTCAGTGGTCTAACCGGCGACACACCGGCGGTCAGACCGGCGGCATCGTGGTGGTCAGACCGGCGGGTGACCTGCGGTCAGACCGGCGGCGGCGACAGG

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	75.70%	24.00%	0.34%	0.00%	NA
All Indica	2759	60.20%	39.30%	0.47%	0.00%	NA
All Japonica	1512	98.20%	1.70%	0.07%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	82.70%	16.80%	0.50%	0.00%	NA
Indica II	465	72.00%	27.50%	0.43%	0.00%	NA
Indica III	913	37.10%	62.40%	0.44%	0.00%	NA
Indica Intermediate	786	63.10%	36.40%	0.51%	0.00%	NA
Temperate Japonica	767	99.50%	0.50%	0.00%	0.00%	NA
Tropical Japonica	504	98.40%	1.40%	0.20%	0.00%	NA
Japonica Intermediate	241	93.80%	6.20%	0.00%	0.00%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	76.70%	21.10%	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
vg0825753695	C -> T	LOC_Os08g40660.1	upstream_gene_variant ; 3321.0bp to feature; MODIFIER	silent_mutation	Average:48.952; most accessible tissue: Zhenshan97 flag leaf, score: 63.101	N	N	N	N
vg0825753695	C -> T	LOC_Os08g40670.1	upstream_gene_variant ; 369.0bp to feature; MODIFIER	silent_mutation	Average:48.952; most accessible tissue: Zhenshan97 flag leaf, score: 63.101	N	N	N	N
vg0825753695	C -> T	LOC_Os08g40670-LOC_Os08g40680	intergenic_region ; MODIFIER	silent_mutation	Average:48.952; most accessible tissue: Zhenshan97 flag leaf, score: 63.101	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0825753695	NA	3.01E-06	mr1536	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
vg0825753695	2.17E-06	NA	mr1033_2	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
vg0825753695	NA	7.59E-07	mr1536_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