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Detailed information for vg1208079291:

Variant ID: vg1208079291 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 8079291
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTAGGATAATTTATGATAAACAATTATGGATAGTTTACTGACCTTGGTTTTTGTACACTAGCTTTTTGGTTCCTTACAACAGTGAGATATTTTACAAGCT[G/A]
CATTTTTCATGTGTTTGCATCCTCTGAATTGGATTTTAATTCATAGTAAAATATTAAGGCAAGTTGTTTAATGTTCATCTCAATTATAAACATTTGTGTT

Reverse complement sequence

AACACAAATGTTTATAATTGAGATGAACATTAAACAACTTGCCTTAATATTTTACTATGAATTAAAATCCAATTCAGAGGATGCAAACACATGAAAAATG[C/T]
AGCTTGTAAAATATCTCACTGTTGTAAGGAACCAAAAAGCTAGTGTACAAAAACCAAGGTCAGTAAACTATCCATAATTGTTTATCATAAATTATCCTAA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	50.40%	19.90%	10.16%	19.47%	NA
All Indica	2759	54.20%	28.10%	11.34%	6.31%	NA
All Japonica	1512	46.00%	7.50%	5.62%	40.94%	NA
Aus	269	33.80%	10.00%	17.10%	39.03%	NA
Indica I	595	36.00%	29.60%	21.51%	12.94%	NA
Indica II	465	45.60%	33.50%	13.76%	7.10%	NA
Indica III	913	69.30%	23.80%	4.93%	1.97%	NA
Indica Intermediate	786	55.60%	28.90%	9.67%	5.85%	NA
Temperate Japonica	767	69.50%	1.20%	3.52%	25.81%	NA
Tropical Japonica	504	18.30%	18.70%	6.94%	56.15%	NA
Japonica Intermediate	241	29.00%	4.10%	9.54%	57.26%	NA
VI/Aromatic	96	46.90%	10.40%	33.33%	9.38%	NA
Intermediate	90	63.30%	17.80%	4.44%	14.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1208079291	G -> DEL	N	N	silent_mutation	Average:23.298; most accessible tissue: Minghui63 panicle, score: 42.799	N	N	N	N
vg1208079291	G -> A	LOC_Os12g14220.1	downstream_gene_variant ; 2476.0bp to feature; MODIFIER	silent_mutation	Average:23.298; most accessible tissue: Minghui63 panicle, score: 42.799	N	N	N	N
vg1208079291	G -> A	LOC_Os12g14230.1	downstream_gene_variant ; 4172.0bp to feature; MODIFIER	silent_mutation	Average:23.298; most accessible tissue: Minghui63 panicle, score: 42.799	N	N	N	N
vg1208079291	G -> A	LOC_Os12g14224.1	intron_variant ; MODIFIER	silent_mutation	Average:23.298; most accessible tissue: Minghui63 panicle, score: 42.799	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1208079291	4.78E-06	5.67E-09	mr1422	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
vg1208079291	NA	5.09E-08	mr1425	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
vg1208079291	NA	1.15E-08	mr1583	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
vg1208079291	NA	9.53E-06	mr1002_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
vg1208079291	NA	5.70E-06	mr1218_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
vg1208079291	NA	4.35E-07	mr1850_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
vg1208079291	NA	8.64E-07	mr1864_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