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Detailed information for vg0728714849:

Variant ID: vg0728714849 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 28714849
Reference Allele: A	Alternative Allele: C
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.92, A: 0.09, others allele: 0.00, population size: 90. )

Flanking Sequence (100 bp) in Reference Genome:

TCATGTTATATAATGTCTGTAGCATCAAATATATTATCACATGAGAAAAATCTGATATGGCAAGAGAGTTAACGAGGGGAGAGGTAAAAAGATGAAGAAA[A/C]
AATTTCTTATGCAAGAAACCATTTCTACACAAGAATTAAGAATGAAAACAAGAGGATAGGTAGATAAAAAAAAAAGATAAAGGAGATGATTAGATGATAA

Reverse complement sequence

TTATCATCTAATCATCTCCTTTATCTTTTTTTTTTATCTACCTATCCTCTTGTTTTCATTCTTAATTCTTGTGTAGAAATGGTTTCTTGCATAAGAAATT[T/G]
TTTCTTCATCTTTTTACCTCTCCCCTCGTTAACTCTCTTGCCATATCAGATTTTTCTCATGTGATAATATATTTGATGCTACAGACATTATATAACATGA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	85.80%	14.10%	0.06%	0.00%	NA
All Indica	2759	85.80%	14.10%	0.11%	0.00%	NA
All Japonica	1512	94.80%	5.20%	0.00%	0.00%	NA
Aus	269	29.70%	70.30%	0.00%	0.00%	NA
Indica I	595	60.20%	39.80%	0.00%	0.00%	NA
Indica II	465	96.30%	3.70%	0.00%	0.00%	NA
Indica III	913	97.30%	2.70%	0.00%	0.00%	NA
Indica Intermediate	786	85.80%	13.90%	0.38%	0.00%	NA
Temperate Japonica	767	90.10%	9.90%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	98.80%	1.20%	0.00%	0.00%	NA
VI/Aromatic	96	95.80%	4.20%	0.00%	0.00%	NA
Intermediate	90	93.30%	6.70%	0.00%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0728714849	A -> C	LOC_Os07g48090.1	downstream_gene_variant ; 1958.0bp to feature; MODIFIER	silent_mutation	Average:67.353; most accessible tissue: Minghui63 flower, score: 83.493	N	N	N	N
vg0728714849	A -> C	LOC_Os07g48090-LOC_Os07g48100	intergenic_region ; MODIFIER	silent_mutation	Average:67.353; most accessible tissue: Minghui63 flower, score: 83.493	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0728714849	NA	1.32E-07	mr1028	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
vg0728714849	5.93E-07	5.93E-07	mr1369	Jap_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
vg0728714849	NA	4.23E-07	mr1453	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
vg0728714849	NA	2.01E-06	mr1648	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
vg0728714849	NA	1.39E-08	mr1652	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
vg0728714849	NA	5.25E-06	mr1296_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
vg0728714849	NA	6.72E-10	mr1510_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
vg0728714849	NA	1.10E-07	mr1702_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