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Detailed information for vg0613801975:

Variant ID: vg0613801975 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 13801975
Reference Allele: A	Alternative Allele: C
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.87, A: 0.14, others allele: 0.00, population size: 55. )

Flanking Sequence (100 bp) in Reference Genome:

CCCAAAAATTAAAATCATATAAAAATGGAATGCTCTCGACCTGTAGATTCCGTTTTTACAAACAGATCTTTAATCCGGCACATCAATTTTTTTCACCAAT[A/C]
TAGAGTCGGACTTTTTTTTGAATTGCATAAAACAGTATGCGTTTCGCTAGTATATCCATCAGCTTTTTCAGCTATTTAGATTAACATTGAACATGTTTCA

Reverse complement sequence

TGAAACATGTTCAATGTTAATCTAAATAGCTGAAAAAGCTGATGGATATACTAGCGAAACGCATACTGTTTTATGCAATTCAAAAAAAAGTCCGACTCTA[T/G]
ATTGGTGAAAAAAATTGATGTGCCGGATTAAAGATCTGTTTGTAAAAACGGAATCTACAGGTCGAGAGCATTCCATTTTTATATGATTTTAATTTTTGGG

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	31.90%	11.00%	27.30%	29.86%	NA
All Indica	2759	2.90%	10.10%	39.47%	47.48%	NA
All Japonica	1512	91.50%	0.90%	6.55%	1.06%	NA
Aus	269	3.00%	48.30%	25.65%	23.05%	NA
Indica I	595	3.70%	3.70%	37.98%	54.62%	NA
Indica II	465	1.70%	7.30%	35.70%	55.27%	NA
Indica III	913	0.70%	16.30%	42.28%	40.74%	NA
Indica Intermediate	786	5.70%	9.40%	39.57%	45.29%	NA
Temperate Japonica	767	96.50%	0.30%	2.09%	1.17%	NA
Tropical Japonica	504	83.90%	1.60%	13.69%	0.79%	NA
Japonica Intermediate	241	91.70%	1.20%	5.81%	1.24%	NA
VI/Aromatic	96	2.10%	85.40%	10.42%	2.08%	NA
Intermediate	90	35.60%	15.60%	25.56%	23.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0613801975	A -> C	LOC_Os06g23650.1	upstream_gene_variant ; 2042.0bp to feature; MODIFIER	silent_mutation	Average:27.638; most accessible tissue: Callus, score: 50.656	N	N	N	N
vg0613801975	A -> C	LOC_Os06g23640-LOC_Os06g23650	intergenic_region ; MODIFIER	silent_mutation	Average:27.638; most accessible tissue: Callus, score: 50.656	N	N	N	N
vg0613801975	A -> DEL	N	N	silent_mutation	Average:27.638; most accessible tissue: Callus, score: 50.656	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0613801975	1.86E-06	1.86E-06	mr1396	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