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Detailed information for vg0612880471:

Variant ID: vg0612880471 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 12880471
Reference Allele: G	Alternative Allele: C
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.93, G: 0.06, others allele: 0.00, population size: 250. )

Flanking Sequence (100 bp) in Reference Genome:

CTTTCGTTGGAGGCAAGTGCATGATGAACTAATTGTGTGATTCATAGATTGTTTGCTCTATCTATCTATTTCCGTTATATTTCTATGTGGTATGTGACTG[G/C]
TTATGTTCAGACTGTTGTTAATGCCATTTAGATTTCAAATTTATCTTATGTCACGACATTATTCATGTTTTATTATTTCGGATGTTTTATTTCTATTATT

Reverse complement sequence

AATAATAGAAATAAAACATCCGAAATAATAAAACATGAATAATGTCGTGACATAAGATAAATTTGAAATCTAAATGGCATTAACAACAGTCTGAACATAA[C/G]
CAGTCACATACCACATAGAAATATAACGGAAATAGATAGATAGAGCAAACAATCTATGAATCACACAATTAGTTCATCATGCACTTGCCTCCAACGAAAG

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	68.70%	31.10%	0.13%	0.08%	NA
All Indica	2759	97.70%	2.10%	0.11%	0.11%	NA
All Japonica	1512	11.20%	88.60%	0.13%	0.07%	NA
Aus	269	84.40%	15.60%	0.00%	0.00%	NA
Indica I	595	97.50%	2.20%	0.17%	0.17%	NA
Indica II	465	97.40%	2.40%	0.00%	0.22%	NA
Indica III	913	99.70%	0.20%	0.11%	0.00%	NA
Indica Intermediate	786	95.80%	3.90%	0.13%	0.13%	NA
Temperate Japonica	767	3.00%	96.70%	0.13%	0.13%	NA
Tropical Japonica	504	23.80%	76.00%	0.20%	0.00%	NA
Japonica Intermediate	241	11.20%	88.80%	0.00%	0.00%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	65.60%	33.30%	1.11%	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
vg0612880471	G -> C	LOC_Os06g22200.1	upstream_gene_variant ; 1165.0bp to feature; MODIFIER	silent_mutation	Average:32.253; most accessible tissue: Minghui63 flag leaf, score: 47.544	N	N	N	N
vg0612880471	G -> C	LOC_Os06g22190-LOC_Os06g22200	intergenic_region ; MODIFIER	silent_mutation	Average:32.253; most accessible tissue: Minghui63 flag leaf, score: 47.544	N	N	N	N
vg0612880471	G -> DEL	N	N	silent_mutation	Average:32.253; most accessible tissue: Minghui63 flag leaf, score: 47.544	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0612880471	8.79E-06	NA	mr1078	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
vg0612880471	NA	5.04E-56	mr1087	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
vg0612880471	NA	5.88E-12	mr1138	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
vg0612880471	5.54E-07	5.54E-07	mr1165	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
vg0612880471	NA	1.10E-07	mr1354	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
vg0612880471	NA	5.06E-36	mr1402	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
vg0612880471	NA	3.95E-20	mr1477	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
vg0612880471	1.14E-07	1.14E-07	mr1478	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
vg0612880471	NA	1.45E-19	mr1541	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
vg0612880471	NA	6.29E-10	mr1581	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
vg0612880471	NA	1.38E-20	mr1588	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
vg0612880471	NA	1.19E-20	mr1971	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
vg0612880471	3.01E-06	NA	mr1973	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
vg0612880471	NA	4.21E-08	mr1165_2	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