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Detailed information for vg0607113275:

Variant ID: vg0607113275 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 7113275
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CTAGCGCCGGTCCCCCCATTTTCCTGTGCGGTTCCACATATGGTCCGCCTGGAAACAAAAGGGTTCGGCGTCCAGAAAAATCTTTCATGTAGTAGTGTGC[A/G]
TAGCATGATGATAAAAGCAGTGCCATTGTACAACCATGACAAAAAACCCGCGGCCGGTGCCGGTAAGTCTTCATTTGTAGTGAATCTGCGAGAGGCGCAG

Reverse complement sequence

CTGCGCCTCTCGCAGATTCACTACAAATGAAGACTTACCGGCACCGGCCGCGGGTTTTTTGTCATGGTTGTACAATGGCACTGCTTTTATCATCATGCTA[T/C]
GCACACTACTACATGAAAGATTTTTCTGGACGCCGAACCCTTTTGTTTCCAGGCGGACCATATGTGGAACCGCACAGGAAAATGGGGGGACCGGCGCTAG

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	95.40%	2.80%	1.82%	0.00%	NA
All Indica	2759	92.50%	4.50%	2.97%	0.00%	NA
All Japonica	1512	99.60%	0.20%	0.20%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.30%	0.00%	0.67%	0.00%	NA
Indica II	465	78.30%	14.00%	7.74%	0.00%	NA
Indica III	913	97.00%	2.30%	0.66%	0.00%	NA
Indica Intermediate	786	90.50%	5.00%	4.58%	0.00%	NA
Temperate Japonica	767	99.50%	0.30%	0.26%	0.00%	NA
Tropical Japonica	504	99.80%	0.00%	0.20%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	96.70%	2.20%	1.11%	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
vg0607113275	A -> G	LOC_Os06g12980-LOC_Os06g12990	intergenic_region ; MODIFIER	silent_mutation	Average:62.397; most accessible tissue: Minghui63 root, score: 72.134	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0607113275	NA	3.65E-06	mr1668	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
vg0607113275	NA	7.61E-06	mr1668_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
vg0607113275	NA	9.00E-06	mr1733_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