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Detailed information for vg0713683070:

Variant ID: vg0713683070 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 13683070
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GCCGTTGTTTTTGTGATTGATTTTATTTAAACTTTTTTCTGAAACAACTAAGGGAGTGCTTCTCAAACGACACGGATGAGACAGTGCGTCTCGTCCGGTC[A/G]
GAGTATGTGCAATGTTTTAGTCTTTTGAATTGATCAAGATTGGCACCCGGCCAACAGCTTTCAAACGGCCACCCAGGCCTGGCTGATCCCATCAGCCGCA

Reverse complement sequence

TGCGGCTGATGGGATCAGCCAGGCCTGGGTGGCCGTTTGAAAGCTGTTGGCCGGGTGCCAATCTTGATCAATTCAAAAGACTAAAACATTGCACATACTC[T/C]
GACCGGACGAGACGCACTGTCTCATCCGTGTCGTTTGAGAAGCACTCCCTTAGTTGTTTCAGAAAAAAGTTTAAATAAAATCAATCACAAAAACAACGGC

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	53.30%	12.00%	13.56%	21.12%	NA
All Indica	2759	68.90%	0.10%	18.41%	12.61%	NA
All Japonica	1512	32.60%	36.80%	1.19%	29.37%	NA
Aus	269	20.40%	0.00%	37.92%	41.64%	NA
Indica I	595	72.40%	0.00%	21.18%	6.39%	NA
Indica II	465	67.70%	0.20%	20.65%	11.40%	NA
Indica III	913	66.80%	0.00%	18.18%	15.01%	NA
Indica Intermediate	786	69.30%	0.10%	15.27%	15.27%	NA
Temperate Japonica	767	48.20%	15.50%	1.69%	34.55%	NA
Tropical Japonica	504	12.50%	78.80%	0.40%	8.33%	NA
Japonica Intermediate	241	24.90%	17.00%	1.24%	56.85%	NA
VI/Aromatic	96	17.70%	0.00%	5.21%	77.08%	NA
Intermediate	90	57.80%	11.10%	8.89%	22.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0713683070	A -> DEL	N	N	silent_mutation	Average:10.25; most accessible tissue: Zhenshan97 root, score: 15.132	N	N	N	N
vg0713683070	A -> G	LOC_Os07g24110-LOC_Os07g24130	intergenic_region ; MODIFIER	silent_mutation	Average:10.25; most accessible tissue: Zhenshan97 root, score: 15.132	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0713683070	NA	5.00E-06	mr1570_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
vg0713683070	1.91E-06	3.45E-06	mr1946_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
vg0713683070	1.91E-06	3.45E-06	mr1948_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