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Detailed information for vg0416107935:

Variant ID: vg0416107935 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 16107935
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.95, T: 0.05, others allele: 0.00, population size: 85. )

Flanking Sequence (100 bp) in Reference Genome:

ATCTCCATCCGTGTACCTTTGTTTATAACCAGACTGAGCCACAAACTAAGCCTTACCCACTAGACATGTGGAAGTACGGTAGTGCTTTGCAATAGAGGCC[T/C]
GAGCTTAATCCTTATATTGGCCGGGTGCTACTTCCCACAACTGGCATGCACCCAAACCCCACCGGAAAATAGGTTTTAGGGGTTTTGAAAGAGAAAGAGA

Reverse complement sequence

TCTCTTTCTCTTTCAAAACCCCTAAAACCTATTTTCCGGTGGGGTTTGGGTGCATGCCAGTTGTGGGAAGTAGCACCCGGCCAATATAAGGATTAAGCTC[A/G]
GGCCTCTATTGCAAAGCACTACCGTACTTCCACATGTCTAGTGGGTAAGGCTTAGTTTGTGGCTCAGTCTGGTTATAAACAAAGGTACACGGATGGAGAT

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	68.90%	17.00%	12.65%	1.46%	NA
All Indica	2759	74.80%	12.70%	10.80%	1.67%	NA
All Japonica	1512	70.40%	28.10%	1.46%	0.07%	NA
Aus	269	15.60%	0.40%	79.18%	4.83%	NA
Indica I	595	92.40%	0.50%	5.55%	1.51%	NA
Indica II	465	79.80%	5.80%	13.98%	0.43%	NA
Indica III	913	57.00%	27.40%	13.14%	2.52%	NA
Indica Intermediate	786	79.40%	8.90%	10.18%	1.53%	NA
Temperate Japonica	767	67.90%	31.80%	0.26%	0.00%	NA
Tropical Japonica	504	68.80%	28.00%	3.17%	0.00%	NA
Japonica Intermediate	241	81.30%	16.60%	1.66%	0.41%	NA
VI/Aromatic	96	19.80%	13.50%	58.33%	8.33%	NA
Intermediate	90	73.30%	15.60%	10.00%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0416107935	T -> C	LOC_Os04g27260.1	upstream_gene_variant ; 119.0bp to feature; MODIFIER	silent_mutation	Average:48.802; most accessible tissue: Minghui63 young leaf, score: 72.408	N	N	N	N
vg0416107935	T -> C	LOC_Os04g27260-LOC_Os04g27270	intergenic_region ; MODIFIER	silent_mutation	Average:48.802; most accessible tissue: Minghui63 young leaf, score: 72.408	N	N	N	N
vg0416107935	T -> DEL	N	N	silent_mutation	Average:48.802; most accessible tissue: Minghui63 young leaf, score: 72.408	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0416107935	2.39E-06	NA	mr1181_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