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Detailed information for vg0714912592:

Variant ID: vg0714912592 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 14912592
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TAGGTCCGTGAACTTGGTTTAATGTACCACCCCCGGTCCAATCGTCCTTTGACCATGTTTGACCACCAATGTGGCATGCTACGTAGGCAACACTTTTGTG[C/A]
TCAGCCCCATCCACATATACCTTCGCACATAACTTGCCATGACCTGTGCATTTCAACCCAAACCCCCCAAAATATCCCTAAATTGGCTAGGGTTTCGATG

Reverse complement sequence

CATCGAAACCCTAGCCAATTTAGGGATATTTTGGGGGGTTTGGGTTGAAATGCACAGGTCATGGCAAGTTATGTGCGAAGGTATATGTGGATGGGGCTGA[G/T]
CACAAAAGTGTTGCCTACGTAGCATGCCACATTGGTGGTCAAACATGGTCAAAGGACGATTGGACCGGGGGTGGTACATTAAACCAAGTTCACGGACCTA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	41.10%	0.50%	3.75%	54.68%	NA
All Indica	2759	10.70%	0.70%	5.76%	82.82%	NA
All Japonica	1512	98.70%	0.00%	0.07%	1.19%	NA
Aus	269	7.80%	0.00%	4.46%	87.73%	NA
Indica I	595	23.90%	0.20%	3.53%	72.44%	NA
Indica II	465	6.50%	1.50%	8.60%	83.44%	NA
Indica III	913	3.60%	0.70%	5.81%	89.92%	NA
Indica Intermediate	786	11.60%	0.60%	5.73%	82.06%	NA
Temperate Japonica	767	98.30%	0.00%	0.00%	1.69%	NA
Tropical Japonica	504	99.40%	0.00%	0.20%	0.40%	NA
Japonica Intermediate	241	98.80%	0.00%	0.00%	1.24%	NA
VI/Aromatic	96	85.40%	0.00%	1.04%	13.54%	NA
Intermediate	90	55.60%	4.40%	4.44%	35.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0714912592	C -> DEL	N	N	silent_mutation	Average:21.496; most accessible tissue: Callus, score: 49.892	N	N	N	N
vg0714912592	C -> A	LOC_Os07g26000.1	upstream_gene_variant ; 3444.0bp to feature; MODIFIER	silent_mutation	Average:21.496; most accessible tissue: Callus, score: 49.892	N	N	N	N
vg0714912592	C -> A	LOC_Os07g25980.1	downstream_gene_variant ; 4963.0bp to feature; MODIFIER	silent_mutation	Average:21.496; most accessible tissue: Callus, score: 49.892	N	N	N	N
vg0714912592	C -> A	LOC_Os07g25990.1	downstream_gene_variant ; 1119.0bp to feature; MODIFIER	silent_mutation	Average:21.496; most accessible tissue: Callus, score: 49.892	N	N	N	N
vg0714912592	C -> A	LOC_Os07g25990-LOC_Os07g26000	intergenic_region ; MODIFIER	silent_mutation	Average:21.496; most accessible tissue: Callus, score: 49.892	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0714912592	4.21E-06	NA	mr1699_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