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Detailed information for vg0815897027:

Variant ID: vg0815897027 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 15897027
Reference Allele: A	Alternative Allele: C
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.01, others allele: 0.00, population size: 254. )

Flanking Sequence (100 bp) in Reference Genome:

GGGGTTAAGATAATCCAAGGGTAGAGTGACACACAAGCATTAACTACTCATTCTCATAATATATTATCTAAGCTAAGTGGAAAGAAAAGAGAAAAAAAAT[A/C]
TATTCCTATACTTCTAATATGCATAGTATACATACATTCTAGTTAACCGAAATACTAGCTAATACCCTCTATCCGATGCCCTCCTAGTACTTCGAGAAGC

Reverse complement sequence

GCTTCTCGAAGTACTAGGAGGGCATCGGATAGAGGGTATTAGCTAGTATTTCGGTTAACTAGAATGTATGTATACTATGCATATTAGAAGTATAGGAATA[T/G]
ATTTTTTTTCTCTTTTCTTTCCACTTAGCTTAGATAATATATTATGAGAATGAGTAGTTAATGCTTGTGTGTCACTCTACCCTTGGATTATCTTAACCCC

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	96.80%	1.10%	1.93%	0.25%	NA
All Indica	2759	99.20%	0.20%	0.40%	0.25%	NA
All Japonica	1512	97.80%	0.70%	1.26%	0.33%	NA
Aus	269	97.00%	0.70%	2.23%	0.00%	NA
Indica I	595	99.70%	0.00%	0.34%	0.00%	NA
Indica II	465	98.90%	0.20%	0.22%	0.65%	NA
Indica III	913	99.20%	0.10%	0.44%	0.22%	NA
Indica Intermediate	786	98.90%	0.40%	0.51%	0.25%	NA
Temperate Japonica	767	99.90%	0.00%	0.13%	0.00%	NA
Tropical Japonica	504	96.00%	1.60%	2.18%	0.20%	NA
Japonica Intermediate	241	94.60%	0.80%	2.90%	1.66%	NA
VI/Aromatic	96	20.80%	29.20%	50.00%	0.00%	NA
Intermediate	90	86.70%	5.60%	7.78%	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
vg0815897027	A -> C	LOC_Os08g26120-LOC_Os08g26140	intergenic_region ; MODIFIER	silent_mutation	Average:41.724; most accessible tissue: Zhenshan97 flag leaf, score: 72.012	N	N	N	N
vg0815897027	A -> DEL	N	N	silent_mutation	Average:41.724; most accessible tissue: Zhenshan97 flag leaf, score: 72.012	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0815897027	NA	1.08E-07	mr1188	Jap_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
vg0815897027	1.90E-08	1.20E-13	mr1188_2	Jap_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