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Detailed information for vg0220269530:

Variant ID: vg0220269530 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 20269530
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.91, T: 0.09, others allele: 0.00, population size: 96. )

Flanking Sequence (100 bp) in Reference Genome:

GCATTTCCCACATTCATATTGATGTTAATGAATCTAGATAGATATATATGTCTAGATTCATTAACATTAATATGAATATGAGAAATGCTAGAATGACTTA[C/T]
ATTGTGAAACGGAGGGAGTATCATTCATGAAGTACATTATTTTACATAGAAAATCTTCCTCTGTTCTCCATGTCACCCTAAAATCTAAATATAACGCTAA

Reverse complement sequence

TTAGCGTTATATTTAGATTTTAGGGTGACATGGAGAACAGAGGAAGATTTTCTATGTAAAATAATGTACTTCATGAATGATACTCCCTCCGTTTCACAAT[G/A]
TAAGTCATTCTAGCATTTCTCATATTCATATTAATGTTAATGAATCTAGACATATATATCTATCTAGATTCATTAACATCAATATGAATGTGGGAAATGC

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	40.50%	11.40%	13.92%	34.26%	NA
All Indica	2759	9.10%	19.00%	21.89%	49.98%	NA
All Japonica	1512	98.30%	0.10%	0.20%	1.39%	NA
Aus	269	7.80%	4.50%	15.99%	71.75%	NA
Indica I	595	15.50%	10.40%	21.18%	52.94%	NA
Indica II	465	11.60%	11.20%	18.71%	58.49%	NA
Indica III	913	4.50%	33.10%	21.91%	40.53%	NA
Indica Intermediate	786	8.30%	13.70%	24.30%	53.69%	NA
Temperate Japonica	767	99.00%	0.00%	0.39%	0.65%	NA
Tropical Japonica	504	98.60%	0.20%	0.00%	1.19%	NA
Japonica Intermediate	241	95.90%	0.00%	0.00%	4.15%	NA
VI/Aromatic	96	95.80%	0.00%	2.08%	2.08%	NA
Intermediate	90	66.70%	0.00%	6.67%	26.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0220269530	C -> T	LOC_Os02g33980-LOC_Os02g33990	intergenic_region ; MODIFIER	silent_mutation	Average:31.375; most accessible tissue: Callus, score: 70.033	N	N	N	N
vg0220269530	C -> DEL	N	N	silent_mutation	Average:31.375; most accessible tissue: Callus, score: 70.033	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0220269530	NA	3.02E-07	mr1312	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
vg0220269530	4.06E-07	4.06E-07	mr1655	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
vg0220269530	NA	6.05E-07	mr1925	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