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Detailed information for vg1217214923:

Variant ID: vg1217214923 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 17214923
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AAAGCAGTAAAACAGTTGCAGTAATTAATCAATATTAACCAATCACTGTCCAATGCTACGCCACGTTGGAGAGAAGTTCACTCCTGAACAGAAGAAAGAC[T/A]
TCAATGCAATGATGCAGCAAACACGAGATCAATTTTTAAGTTCATTCATGCAAACTCGCAAGGGCACATTTGTTCAGAAGTACAAGCTGAAGGTGGTTCC

Reverse complement sequence

GGAACCACCTTCAGCTTGTACTTCTGAACAAATGTGCCCTTGCGAGTTTGCATGAATGAACTTAAAAATTGATCTCGTGTTTGCTGCATCATTGCATTGA[A/T]
GTCTTTCTTCTGTTCAGGAGTGAACTTCTCTCCAACGTGGCGTAGCATTGGACAGTGATTGGTTAATATTGATTAATTACTGCAACTGTTTTACTGCTTT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	89.70%	0.30%	0.78%	9.25%	NA
All Indica	2759	85.20%	0.40%	1.05%	13.34%	NA
All Japonica	1512	95.20%	0.00%	0.46%	4.37%	NA
Aus	269	99.30%	0.00%	0.00%	0.74%	NA
Indica I	595	95.50%	0.20%	0.17%	4.20%	NA
Indica II	465	64.90%	1.10%	2.15%	31.83%	NA
Indica III	913	90.90%	0.10%	0.77%	8.21%	NA
Indica Intermediate	786	82.70%	0.60%	1.40%	15.27%	NA
Temperate Japonica	767	97.70%	0.00%	0.00%	2.35%	NA
Tropical Japonica	504	93.10%	0.00%	0.79%	6.15%	NA
Japonica Intermediate	241	91.70%	0.00%	1.24%	7.05%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	97.80%	0.00%	1.11%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1217214923	T -> DEL	N	N	silent_mutation	Average:40.817; most accessible tissue: Minghui63 young leaf, score: 68.07	N	N	N	N
vg1217214923	T -> A	LOC_Os12g29070.1	intron_variant ; MODIFIER	silent_mutation	Average:40.817; most accessible tissue: Minghui63 young leaf, score: 68.07	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1217214923	NA	5.46E-06	mr1024	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
vg1217214923	2.00E-07	NA	mr1183	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
vg1217214923	2.00E-06	NA	mr1183	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
vg1217214923	1.00E-06	NA	mr1503	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
vg1217214923	4.50E-06	NA	mr1503	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