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Detailed information for vg0709806584:

Variant ID: vg0709806584 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 9806584
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACATCATGTCACCATGTGCCTCAATACCACCACGGTACCTCGGAAAGGAGCTGTGACAATACCCCTTGCATAACACAATTCCACCGCAGCGCACCTTTCG[T/C]
GGATCATAATCACCACCTTATAAACAAGGCATGGACTCCCCAGCGACCCCCGTGGGGCTTATCTCCGCCACTTCTCAGTCTGGTGCTCCGCAATGAACCA

Reverse complement sequence

TGGTTCATTGCGGAGCACCAGACTGAGAAGTGGCGGAGATAAGCCCCACGGGGGTCGCTGGGGAGTCCATGCCTTGTTTATAAGGTGGTGATTATGATCC[A/G]
CGAAAGGTGCGCTGCGGTGGAATTGTGTTATGCAAGGGGTATTGTCACAGCTCCTTTCCGAGGTACCGTGGTGGTATTGAGGCACATGGTGACATGATGT

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	41.20%	0.20%	0.85%	57.74%	NA
All Indica	2759	18.30%	0.20%	1.01%	80.43%	NA
All Japonica	1512	77.40%	0.10%	0.66%	21.76%	NA
Aus	269	64.30%	0.00%	0.37%	35.32%	NA
Indica I	595	36.00%	0.20%	1.01%	62.86%	NA
Indica II	465	15.70%	0.90%	1.08%	82.37%	NA
Indica III	913	3.80%	0.00%	1.20%	94.96%	NA
Indica Intermediate	786	23.40%	0.10%	0.76%	75.70%	NA
Temperate Japonica	767	76.90%	0.10%	0.39%	22.56%	NA
Tropical Japonica	504	89.30%	0.20%	0.60%	9.92%	NA
Japonica Intermediate	241	54.40%	0.00%	1.66%	43.98%	NA
VI/Aromatic	96	61.50%	0.00%	0.00%	38.54%	NA
Intermediate	90	44.40%	0.00%	1.11%	54.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0709806584	T -> DEL	N	N	silent_mutation	Average:14.573; most accessible tissue: Callus, score: 25.737	N	N	N	N
vg0709806584	T -> C	LOC_Os07g16710-LOC_Os07g16720	intergenic_region ; MODIFIER	silent_mutation	Average:14.573; most accessible tissue: Callus, score: 25.737	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0709806584	3.95E-07	NA	mr1971	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
vg0709806584	2.85E-06	NA	mr1222_2	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