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Detailed information for vg0115948322:

Variant ID: vg0115948322 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 15948322
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.94, T: 0.07, others allele: 0.00, population size: 108. )

Flanking Sequence (100 bp) in Reference Genome:

GAACAACAAAAAAAAGACTGAATTTTAATACATTTATACTTTTCAAATTGTCAAAAAAAATTGATACGGCTAAAATATAATGAATGAGGTTATGAATTTA[C/T]
GCATCGGTTTAATACTATTGGCTGTATAGTTTTGTTTTAAAATTTCTGATAAAATAGTTCGTTGTCGTGCATGATGTGTACACGAAAGCTTTGTCCACAA

Reverse complement sequence

TTGTGGACAAAGCTTTCGTGTACACATCATGCACGACAACGAACTATTTTATCAGAAATTTTAAAACAAAACTATACAGCCAATAGTATTAAACCGATGC[G/A]
TAAATTCATAACCTCATTCATTATATTTTAGCCGTATCAATTTTTTTTGACAATTTGAAAAGTATAAATGTATTAAAATTCAGTCTTTTTTTTGTTGTTC

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	47.00%	39.90%	0.23%	12.80%	NA
All Indica	2759	72.10%	6.10%	0.40%	21.49%	NA
All Japonica	1512	2.40%	97.40%	0.00%	0.20%	NA
Aus	269	61.00%	39.00%	0.00%	0.00%	NA
Indica I	595	50.60%	1.30%	0.50%	47.56%	NA
Indica II	465	56.30%	15.70%	0.22%	27.74%	NA
Indica III	913	95.50%	1.60%	0.11%	2.74%	NA
Indica Intermediate	786	70.40%	9.00%	0.76%	19.85%	NA
Temperate Japonica	767	1.00%	99.00%	0.00%	0.00%	NA
Tropical Japonica	504	5.00%	94.60%	0.00%	0.40%	NA
Japonica Intermediate	241	1.70%	97.90%	0.00%	0.41%	NA
VI/Aromatic	96	6.20%	93.80%	0.00%	0.00%	NA
Intermediate	90	30.00%	60.00%	0.00%	10.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0115948322	C -> T	LOC_Os01g28474.1	upstream_gene_variant ; 454.0bp to feature; MODIFIER	silent_mutation	Average:36.131; most accessible tissue: Callus, score: 58.893	N	N	N	N
vg0115948322	C -> T	LOC_Os01g28450-LOC_Os01g28474	intergenic_region ; MODIFIER	silent_mutation	Average:36.131; most accessible tissue: Callus, score: 58.893	N	N	N	N
vg0115948322	C -> DEL	N	N	silent_mutation	Average:36.131; most accessible tissue: Callus, score: 58.893	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0115948322	NA	5.74E-11	mr1514	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
vg0115948322	5.20E-06	NA	mr1711	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
vg0115948322	NA	6.18E-06	mr1711	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