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Detailed information for vg0707270813:

Variant ID: vg0707270813 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 7270813
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AATGTTATTCTGGATGGCATAATAAATGTGCACCTCTGATAGCTCCTCACATCTAATCATATCCATCATTGTGCTCACCTATGTTATATTTAGTGGTGGA[A/G]
ATTTAAAGTTTCAGGTTGGATATATCCCTTTCCAGAGTTCAGATCTTGCATGGGCGACAGGTATCATTATAATGATGAGTTCAGGTTGTTTATTTTGCAG

Reverse complement sequence

CTGCAAAATAAACAACCTGAACTCATCATTATAATGATACCTGTCGCCCATGCAAGATCTGAACTCTGGAAAGGGATATATCCAACCTGAAACTTTAAAT[T/C]
TCCACCACTAAATATAACATAGGTGAGCACAATGATGGATATGATTAGATGTGAGGAGCTATCAGAGGTGCACATTTATTATGCCATCCAGAATAACATT

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	94.20%	5.00%	0.76%	0.00%	NA
All Indica	2759	99.70%	0.10%	0.14%	0.00%	NA
All Japonica	1512	82.80%	15.10%	2.05%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.60%	0.40%	0.00%	0.00%	NA
Indica III	913	99.90%	0.10%	0.00%	0.00%	NA
Indica Intermediate	786	99.40%	0.10%	0.51%	0.00%	NA
Temperate Japonica	767	79.50%	17.70%	2.74%	0.00%	NA
Tropical Japonica	504	94.20%	5.00%	0.79%	0.00%	NA
Japonica Intermediate	241	69.30%	28.20%	2.49%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	94.40%	4.40%	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
vg0707270813	A -> G	LOC_Os07g12720.1	downstream_gene_variant ; 1421.0bp to feature; MODIFIER	silent_mutation	Average:57.081; most accessible tissue: Callus, score: 82.71	N	N	N	N
vg0707270813	A -> G	LOC_Os07g12730.1	downstream_gene_variant ; 2043.0bp to feature; MODIFIER	silent_mutation	Average:57.081; most accessible tissue: Callus, score: 82.71	N	N	N	N
vg0707270813	A -> G	LOC_Os07g12720-LOC_Os07g12730	intergenic_region ; MODIFIER	silent_mutation	Average:57.081; most accessible tissue: Callus, score: 82.71	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0707270813	NA	1.02E-07	mr1097	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
vg0707270813	5.84E-07	5.84E-07	mr1128	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
vg0707270813	NA	7.08E-06	mr1092_2	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