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Detailed information for vg0707143185:

Variant ID: vg0707143185 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 7143185
Reference Allele: C	Alternative Allele: A
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 117. )

Flanking Sequence (100 bp) in Reference Genome:

TGGATGGCTTCAAATTATCGGAAGTTTTAATTTGTGCATCAGAATTTCTTATGTGTAAAATCCTAGGTCAAAGCATGTGTGTTGTTACTGTTAGGTTTTT[C/A]
TTTTTGAAATGACCGGAAGTTCTGATGTCCACATCAGAATTTATGATGTTGTAATCTTTTTATCCCAATGGCAAAAATCTGGATATGTTGTTTAAATCCC

Reverse complement sequence

GGGATTTAAACAACATATCCAGATTTTTGCCATTGGGATAAAAAGATTACAACATCATAAATTCTGATGTGGACATCAGAACTTCCGGTCATTTCAAAAA[G/T]
AAAAACCTAACAGTAACAACACACATGCTTTGACCTAGGATTTTACACATAAGAAATTCTGATGCACAAATTAAAACTTCCGATAATTTGAAGCCATCCA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	81.10%	16.90%	2.03%	0.00%	NA
All Indica	2759	98.00%	1.80%	0.14%	0.00%	NA
All Japonica	1512	46.20%	48.50%	5.29%	0.00%	NA
Aus	269	95.50%	1.50%	2.97%	0.00%	NA
Indica I	595	99.50%	0.20%	0.34%	0.00%	NA
Indica II	465	94.80%	5.20%	0.00%	0.00%	NA
Indica III	913	99.70%	0.30%	0.00%	0.00%	NA
Indica Intermediate	786	96.80%	2.90%	0.25%	0.00%	NA
Temperate Japonica	767	13.40%	78.60%	7.95%	0.00%	NA
Tropical Japonica	504	87.70%	9.90%	2.38%	0.00%	NA
Japonica Intermediate	241	63.90%	33.20%	2.90%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	83.30%	12.20%	4.44%	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
vg0707143185	C -> A	LOC_Os07g12510.1	upstream_gene_variant ; 2410.0bp to feature; MODIFIER	silent_mutation	Average:34.995; most accessible tissue: Callus, score: 55.283	N	N	N	N
vg0707143185	C -> A	LOC_Os07g12520.1	upstream_gene_variant ; 2354.0bp to feature; MODIFIER	silent_mutation	Average:34.995; most accessible tissue: Callus, score: 55.283	N	N	N	N
vg0707143185	C -> A	LOC_Os07g12510-LOC_Os07g12520	intergenic_region ; MODIFIER	silent_mutation	Average:34.995; most accessible tissue: Callus, score: 55.283	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0707143185	NA	7.46E-09	mr1552	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
vg0707143185	6.73E-07	NA	mr1672_2	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
vg0707143185	NA	9.72E-07	mr1672_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