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Detailed information for vg1215431363:

Variant ID: vg1215431363 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 15431363
Reference Allele: C	Alternative Allele: G
Primary Allele: G	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, G: 0.03, others allele: 0.00, population size: 111. )

Flanking Sequence (100 bp) in Reference Genome:

TTAAAAAATTCTCTTGGTTATTTTGTGCTAGAGGTTATTTGAGAAAGAGTGATAAATGCAATAGGTATATGTGTTTCGTGTTTATTCTTCAACGTATGTG[C/G]
TTGTTAAGATGTTGCATTATAAATCGTATGAAATCACGAATTTTGATTGTTGATTCAAGCTTAATTGTAAAATCTTTGGTTCATGGTTATACTTTAATTC

Reverse complement sequence

GAATTAAAGTATAACCATGAACCAAAGATTTTACAATTAAGCTTGAATCAACAATCAAAATTCGTGATTTCATACGATTTATAATGCAACATCTTAACAA[G/C]
CACATACGTTGAAGAATAAACACGAAACACATATACCTATTGCATTTATCACTCTTTCTCAAATAACCTCTAGCACAAAATAACCAAGAGAATTTTTTAA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	32.60%	23.10%	4.13%	40.12%	NA
All Indica	2759	54.30%	5.00%	4.02%	36.72%	NA
All Japonica	1512	1.50%	59.60%	0.40%	38.56%	NA
Aus	269	0.70%	7.10%	24.16%	68.03%	NA
Indica I	595	77.80%	3.70%	1.34%	17.14%	NA
Indica II	465	60.40%	4.30%	1.51%	33.76%	NA
Indica III	913	34.10%	4.30%	7.45%	54.22%	NA
Indica Intermediate	786	56.20%	7.30%	3.56%	32.95%	NA
Temperate Japonica	767	1.00%	91.30%	0.26%	7.43%	NA
Tropical Japonica	504	1.80%	10.70%	0.60%	86.90%	NA
Japonica Intermediate	241	2.10%	61.00%	0.41%	36.51%	NA
VI/Aromatic	96	2.10%	10.40%	4.17%	83.33%	NA
Intermediate	90	21.10%	27.80%	10.00%	41.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1215431363	C -> DEL	N	N	silent_mutation	Average:13.223; most accessible tissue: Zhenshan97 root, score: 22.162	N	N	N	N
vg1215431363	C -> G	LOC_Os12g26400.1	downstream_gene_variant ; 616.0bp to feature; MODIFIER	silent_mutation	Average:13.223; most accessible tissue: Zhenshan97 root, score: 22.162	N	N	N	N
vg1215431363	C -> G	LOC_Os12g26410.1	downstream_gene_variant ; 1585.0bp to feature; MODIFIER	silent_mutation	Average:13.223; most accessible tissue: Zhenshan97 root, score: 22.162	N	N	N	N
vg1215431363	C -> G	LOC_Os12g26400-LOC_Os12g26410	intergenic_region ; MODIFIER	silent_mutation	Average:13.223; most accessible tissue: Zhenshan97 root, score: 22.162	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1215431363	1.52E-06	6.98E-07	mr1035	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
vg1215431363	NA	2.87E-06	mr1058	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
vg1215431363	NA	4.95E-06	mr1251	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
vg1215431363	NA	1.48E-06	mr1330	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
vg1215431363	4.55E-06	1.42E-07	mr1438	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
vg1215431363	NA	5.78E-10	mr1457	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
vg1215431363	NA	2.83E-06	mr1568	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
vg1215431363	NA	9.97E-06	mr1577	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
vg1215431363	2.34E-06	2.14E-07	mr1579	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
vg1215431363	NA	4.32E-09	mr1610	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
vg1215431363	4.62E-06	3.04E-06	mr1626	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
vg1215431363	8.72E-06	1.82E-06	mr1686	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
vg1215431363	NA	4.52E-08	mr1785	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
vg1215431363	NA	1.22E-08	mr1836	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
vg1215431363	NA	4.05E-10	mr1023_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
vg1215431363	9.12E-06	3.22E-12	mr1055_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