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Detailed information for vg0906731412:

Variant ID: vg0906731412 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 6731412
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 263. )

Flanking Sequence (100 bp) in Reference Genome:

GACTACATGTTTAGTTTTTTAACTAACCACATAGTCGGGGGCTACACCTAATTAGGTGCATCTACTCGATGCACCCAGTTTTATTTCTTTTTTCGCCCTT[C/T]
ACAGTTTTTGATTTTAGTACTCGGCATACCAGAGCAGAAGGAATTGAAGCACTCGGATCATTGCTTTATGTTCTGAGAGAAGGCCATTTCGTCGACTGTA

Reverse complement sequence

TACAGTCGACGAAATGGCCTTCTCTCAGAACATAAAGCAATGATCCGAGTGCTTCAATTCCTTCTGCTCTGGTATGCCGAGTACTAAAATCAAAAACTGT[G/A]
AAGGGCGAAAAAAGAAATAAAACTGGGTGCATCGAGTAGATGCACCTAATTAGGTGTAGCCCCCGACTATGTGGTTAGTTAAAAAACTAAACATGTAGTC

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	96.50%	1.60%	0.59%	1.35%	NA
All Indica	2759	94.10%	2.60%	0.98%	2.28%	NA
All Japonica	1512	99.80%	0.10%	0.00%	0.07%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	93.40%	5.40%	0.67%	0.50%	NA
Indica II	465	95.10%	0.40%	0.86%	3.66%	NA
Indica III	913	93.20%	2.40%	1.10%	3.29%	NA
Indica Intermediate	786	95.20%	2.00%	1.15%	1.65%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.60%	0.40%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.00%	0.00%	0.41%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	97.80%	1.10%	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
vg0906731412	C -> DEL	N	N	silent_mutation	Average:37.381; most accessible tissue: Minghui63 flag leaf, score: 54.348	N	N	N	N
vg0906731412	C -> T	LOC_Os09g11950.1	upstream_gene_variant ; 922.0bp to feature; MODIFIER	silent_mutation	Average:37.381; most accessible tissue: Minghui63 flag leaf, score: 54.348	N	N	N	N
vg0906731412	C -> T	LOC_Os09g11940.1	downstream_gene_variant ; 4766.0bp to feature; MODIFIER	silent_mutation	Average:37.381; most accessible tissue: Minghui63 flag leaf, score: 54.348	N	N	N	N
vg0906731412	C -> T	LOC_Os09g11950-LOC_Os09g11960	intergenic_region ; MODIFIER	silent_mutation	Average:37.381; most accessible tissue: Minghui63 flag leaf, score: 54.348	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0906731412	NA	6.39E-06	mr1758	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
vg0906731412	NA	3.39E-06	mr1973	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