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Detailed information for vg0616370853:

Variant ID: vg0616370853 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 16370853
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.94, T: 0.05, others allele: 0.00, population size: 92. )

Flanking Sequence (100 bp) in Reference Genome:

CTTGTGATTGACTCCTCAATAACCTTTGGCATGGCCATGCACTTCCATAATCTACAACATCGAGGGGCCCAGAGATATCTCTCCATAGGAGGGGCAAATC[T/C]
CATCTTGATTATTCATATCCCACTACATGTTTCATAGCATACCCAAAAACTACTTTTATAACTACCCAATTACGGAGTAGCGTTTAGCAGTCCCTAAGTA

Reverse complement sequence

TACTTAGGGACTGCTAAACGCTACTCCGTAATTGGGTAGTTATAAAAGTAGTTTTTGGGTATGCTATGAAACATGTAGTGGGATATGAATAATCAAGATG[A/G]
GATTTGCCCCTCCTATGGAGAGATATCTCTGGGCCCCTCGATGTTGTAGATTATGGAAGTGCATGGCCATGCCAAAGGTTATTGAGGAGTCAATCACAAG

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	89.30%	3.10%	7.45%	0.13%	NA
All Indica	2759	89.40%	2.90%	7.43%	0.22%	NA
All Japonica	1512	99.10%	0.30%	0.60%	0.00%	NA
Aus	269	40.50%	17.80%	41.64%	0.00%	NA
Indica I	595	85.20%	4.40%	10.42%	0.00%	NA
Indica II	465	86.20%	3.70%	9.89%	0.22%	NA
Indica III	913	95.80%	1.60%	1.97%	0.55%	NA
Indica Intermediate	786	87.00%	2.90%	10.05%	0.00%	NA
Temperate Japonica	767	99.00%	0.40%	0.65%	0.00%	NA
Tropical Japonica	504	99.20%	0.40%	0.40%	0.00%	NA
Japonica Intermediate	241	99.20%	0.00%	0.83%	0.00%	NA
VI/Aromatic	96	72.90%	8.30%	18.75%	0.00%	NA
Intermediate	90	86.70%	4.40%	8.89%	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
vg0616370853	T -> C	LOC_Os06g28740.1	upstream_gene_variant ; 4390.0bp to feature; MODIFIER	silent_mutation	Average:23.607; most accessible tissue: Zhenshan97 panicle, score: 43.098	N	N	N	N
vg0616370853	T -> C	LOC_Os06g28750.1	downstream_gene_variant ; 545.0bp to feature; MODIFIER	silent_mutation	Average:23.607; most accessible tissue: Zhenshan97 panicle, score: 43.098	N	N	N	N
vg0616370853	T -> C	LOC_Os06g28740-LOC_Os06g28750	intergenic_region ; MODIFIER	silent_mutation	Average:23.607; most accessible tissue: Zhenshan97 panicle, score: 43.098	N	N	N	N
vg0616370853	T -> DEL	N	N	silent_mutation	Average:23.607; most accessible tissue: Zhenshan97 panicle, score: 43.098	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0616370853	1.56E-06	NA	mr1439	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
vg0616370853	6.01E-06	1.62E-06	mr1741	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