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Detailed information for vg1204021683:

Variant ID: vg1204021683 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 4021683
Reference Allele: T	Alternative Allele: G
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GAGGAATGAGATTGGTTTATGGACCTGATTTGTAGTGACCTCAAAGTTGGCACATGAGATGGCTGGGTCTTCATTTCAGACCAACAGAAGGTAATATGTT[T/G]
ACTACTCTTGAGTTTCAAACATTCTGCTATTGAGACCTGAATACATGTTACTGACTTAAAAATATTCTTCAATTACAGGGTATCATTAATGCTGTGCGGA

Reverse complement sequence

TCCGCACAGCATTAATGATACCCTGTAATTGAAGAATATTTTTAAGTCAGTAACATGTATTCAGGTCTCAATAGCAGAATGTTTGAAACTCAAGAGTAGT[A/C]
AACATATTACCTTCTGTTGGTCTGAAATGAAGACCCAGCCATCTCATGTGCCAACTTTGAGGTCACTACAAATCAGGTCCATAAACCAATCTCATTCCTC

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	27.90%	6.50%	0.40%	65.21%	NA
All Indica	2759	7.40%	0.40%	0.36%	91.77%	NA
All Japonica	1512	62.90%	19.00%	0.26%	17.79%	NA
Aus	269	11.50%	0.00%	1.86%	86.62%	NA
Indica I	595	2.00%	0.20%	0.34%	97.48%	NA
Indica II	465	18.50%	0.60%	0.43%	80.43%	NA
Indica III	913	4.70%	0.10%	0.22%	94.96%	NA
Indica Intermediate	786	8.10%	0.90%	0.51%	90.46%	NA
Temperate Japonica	767	83.40%	11.90%	0.26%	4.43%	NA
Tropical Japonica	504	42.30%	26.40%	0.00%	31.35%	NA
Japonica Intermediate	241	40.70%	26.60%	0.83%	31.95%	NA
VI/Aromatic	96	85.40%	0.00%	0.00%	14.58%	NA
Intermediate	90	54.40%	7.80%	0.00%	37.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1204021683	T -> DEL	N	N	silent_mutation	Average:12.225; most accessible tissue: Callus, score: 69.428	N	N	N	N
vg1204021683	T -> G	LOC_Os12g07910.1	downstream_gene_variant ; 2216.0bp to feature; MODIFIER	silent_mutation	Average:12.225; most accessible tissue: Callus, score: 69.428	N	N	N	N
vg1204021683	T -> G	LOC_Os12g07920.1	downstream_gene_variant ; 275.0bp to feature; MODIFIER	silent_mutation	Average:12.225; most accessible tissue: Callus, score: 69.428	N	N	N	N
vg1204021683	T -> G	LOC_Os12g07930.1	downstream_gene_variant ; 1001.0bp to feature; MODIFIER	silent_mutation	Average:12.225; most accessible tissue: Callus, score: 69.428	N	N	N	N
vg1204021683	T -> G	LOC_Os12g07920-LOC_Os12g07930	intergenic_region ; MODIFIER	silent_mutation	Average:12.225; most accessible tissue: Callus, score: 69.428	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1204021683	NA	1.12E-06	mr1345	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
vg1204021683	NA	8.14E-06	mr1653	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
vg1204021683	4.00E-06	3.98E-06	mr1856	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