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Detailed information for vg0907912674:

Variant ID: vg0907912674 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 7912674
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.00, others allele: 0.00, population size: 259. )

Flanking Sequence (100 bp) in Reference Genome:

GTCTAGCCGCAACCCTGCATCCAACGGCGCCAGGATGGGTTCGGCCGAACCAGGGGCCGACCCATTTTCGGCTAGCGGCCTCGTCTTCTGTTGCTCACTT[C/T]
AGACTTGTGAATTTTGGCCCAATTGGTCATGTCATTTTTGCATTCTTGACCTATTCATTGATAGGTCTGATTCTCGACATTGTCTGATTGAATGATCACT

Reverse complement sequence

AGTGATCATTCAATCAGACAATGTCGAGAATCAGACCTATCAATGAATAGGTCAAGAATGCAAAAATGACATGACCAATTGGGCCAAAATTCACAAGTCT[G/A]
AAGTGAGCAACAGAAGACGAGGCCGCTAGCCGAAAATGGGTCGGCCCCTGGTTCGGCCGAACCCATCCTGGCGCCGTTGGATGCAGGGTTGCGGCTAGAC

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	70.90%	11.20%	1.25%	16.59%	NA
All Indica	2759	87.10%	5.50%	0.83%	6.52%	NA
All Japonica	1512	43.80%	21.90%	2.12%	32.14%	NA
Aus	269	79.60%	14.50%	0.37%	5.58%	NA
Indica I	595	96.30%	3.50%	0.17%	0.00%	NA
Indica II	465	87.50%	10.10%	0.43%	1.94%	NA
Indica III	913	81.20%	1.80%	1.42%	15.66%	NA
Indica Intermediate	786	86.80%	8.80%	0.89%	3.56%	NA
Temperate Japonica	767	76.40%	9.00%	1.96%	12.65%	NA
Tropical Japonica	504	5.60%	23.20%	2.98%	68.25%	NA
Japonica Intermediate	241	20.30%	60.20%	0.83%	18.67%	NA
VI/Aromatic	96	10.40%	1.00%	1.04%	87.50%	NA
Intermediate	90	70.00%	6.70%	2.22%	21.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0907912674	C -> DEL	N	N	silent_mutation	Average:55.526; most accessible tissue: Minghui63 panicle, score: 77.956	N	N	N	N
vg0907912674	C -> T	LOC_Os09g13610.1	upstream_gene_variant ; 1409.0bp to feature; MODIFIER	silent_mutation	Average:55.526; most accessible tissue: Minghui63 panicle, score: 77.956	N	N	N	N
vg0907912674	C -> T	LOC_Os09g13610.3	upstream_gene_variant ; 1602.0bp to feature; MODIFIER	silent_mutation	Average:55.526; most accessible tissue: Minghui63 panicle, score: 77.956	N	N	N	N
vg0907912674	C -> T	LOC_Os09g13600-LOC_Os09g13610	intergenic_region ; MODIFIER	silent_mutation	Average:55.526; most accessible tissue: Minghui63 panicle, score: 77.956	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0907912674	2.39E-06	2.39E-06	mr1192_2	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
vg0907912674	NA	5.93E-06	mr1621_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
vg0907912674	3.92E-06	3.93E-06	mr1634_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