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Detailed information for vg1216282319:

Variant ID: vg1216282319 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 16282319
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 104. )

Flanking Sequence (100 bp) in Reference Genome:

TGCTGTGGGAGTCCACAAGTGGGCCAATCAAAACTCGCTACCCCTCCCAGGGCCCGTGCTGGAACGGTGTGTGTGAAAATGTGAATTACCAGTGCAACAA[C/T]
GGTGTGTGTAAAAATGTTATAAAGCACATAATCAGTATTCGGCAAACCCACATTATCGCCACAAACAACAATCTTATTCGTGAAACAGTCGACGGTACAA

Reverse complement sequence

TTGTACCGTCGACTGTTTCACGAATAAGATTGTTGTTTGTGGCGATAATGTGGGTTTGCCGAATACTGATTATGTGCTTTATAACATTTTTACACACACC[G/A]
TTGTTGCACTGGTAATTCACATTTTCACACACACCGTTCCAGCACGGGCCCTGGGAGGGGTAGCGAGTTTTGATTGGCCCACTTGTGGACTCCCACAGCA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	56.00%	33.30%	0.32%	10.30%	NA
All Indica	2759	85.60%	9.50%	0.25%	4.68%	NA
All Japonica	1512	15.50%	70.80%	0.26%	13.36%	NA
Aus	269	4.10%	39.80%	0.74%	55.39%	NA
Indica I	595	93.80%	2.50%	0.17%	3.53%	NA
Indica II	465	66.20%	23.40%	0.00%	10.32%	NA
Indica III	913	91.50%	5.70%	0.22%	2.63%	NA
Indica Intermediate	786	84.00%	10.90%	0.51%	4.58%	NA
Temperate Japonica	767	2.30%	97.40%	0.00%	0.26%	NA
Tropical Japonica	504	37.10%	25.20%	0.79%	36.90%	NA
Japonica Intermediate	241	12.40%	81.70%	0.00%	5.81%	NA
VI/Aromatic	96	7.30%	91.70%	0.00%	1.04%	NA
Intermediate	90	37.80%	53.30%	2.22%	6.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1216282319	C -> DEL	N	N	silent_mutation	Average:29.933; most accessible tissue: Zhenshan97 flag leaf, score: 69.582	N	N	N	N
vg1216282319	C -> T	LOC_Os12g27650.1	downstream_gene_variant ; 2438.0bp to feature; MODIFIER	silent_mutation	Average:29.933; most accessible tissue: Zhenshan97 flag leaf, score: 69.582	N	N	N	N
vg1216282319	C -> T	LOC_Os12g27650-LOC_Os12g27670	intergenic_region ; MODIFIER	silent_mutation	Average:29.933; most accessible tissue: Zhenshan97 flag leaf, score: 69.582	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1216282319	4.33E-06	NA	mr1017	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
vg1216282319	7.83E-08	3.26E-09	mr1268	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
vg1216282319	NA	3.25E-06	mr1304	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
vg1216282319	NA	3.30E-07	mr1364	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
vg1216282319	NA	4.37E-06	mr1364	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
vg1216282319	NA	2.76E-06	mr1443	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
vg1216282319	NA	2.03E-06	mr1622	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
vg1216282319	NA	3.75E-13	mr1940	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
vg1216282319	3.64E-06	NA	mr1022_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
vg1216282319	6.68E-06	NA	mr1055_2	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
vg1216282319	2.05E-07	NA	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
vg1216282319	4.84E-06	NA	mr1079_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
vg1216282319	4.68E-06	NA	mr1132_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
vg1216282319	NA	1.73E-14	mr1133_2	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
vg1216282319	NA	2.63E-07	mr1227_2	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
vg1216282319	1.47E-06	NA	mr1390_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
vg1216282319	1.42E-06	NA	mr1490_2	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
vg1216282319	8.18E-08	NA	mr1490_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