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Detailed information for vg0910687363:

Variant ID: vg0910687363 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 10687363
Reference Allele: G	Alternative Allele: C
Primary Allele: G	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTGGCACGGTTAATGTTTCACAACAGTAGCTCGCGAACCGGTCCTTAATTGTCATGAGCACAACCATCAAAACCATATGCTCACAACCCACCTTTAATCA[G/C]
GTTTTAATTATCAATTAATTAACATTACACATTGACCATCGTGAGCTACCATTAAATATAATCATAATTAATAATGTAATATACTTTATCCCATTAATGA

Reverse complement sequence

TCATTAATGGGATAAAGTATATTACATTATTAATTATGATTATATTTAATGGTAGCTCACGATGGTCAATGTGTAATGTTAATTAATTGATAATTAAAAC[C/G]
TGATTAAAGGTGGGTTGTGAGCATATGGTTTTGATGGTTGTGCTCATGACAATTAAGGACCGGTTCGCGAGCTACTGTTGTGAAACATTAACCGTGCCAA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	26.50%	3.20%	30.70%	39.67%	NA
All Indica	2759	16.10%	5.30%	41.28%	37.30%	NA
All Japonica	1512	49.60%	0.10%	3.57%	46.76%	NA
Aus	269	6.30%	0.00%	60.59%	33.09%	NA
Indica I	595	33.60%	0.00%	20.17%	46.22%	NA
Indica II	465	13.30%	3.70%	35.48%	47.53%	NA
Indica III	913	3.70%	12.50%	60.24%	23.55%	NA
Indica Intermediate	786	19.00%	1.90%	38.68%	40.46%	NA
Temperate Japonica	767	70.30%	0.00%	1.69%	28.03%	NA
Tropical Japonica	504	23.00%	0.20%	6.35%	70.44%	NA
Japonica Intermediate	241	39.40%	0.00%	3.73%	56.85%	NA
VI/Aromatic	96	15.60%	1.00%	70.83%	12.50%	NA
Intermediate	90	26.70%	1.10%	30.00%	42.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0910687363	G -> DEL	N	N	silent_mutation	Average:28.127; most accessible tissue: Zhenshan97 panicle, score: 46.362	N	N	N	N
vg0910687363	G -> C	LOC_Os09g17470.1	upstream_gene_variant ; 2011.0bp to feature; MODIFIER	silent_mutation	Average:28.127; most accessible tissue: Zhenshan97 panicle, score: 46.362	N	N	N	N
vg0910687363	G -> C	LOC_Os09g17470-LOC_Os09g17480	intergenic_region ; MODIFIER	silent_mutation	Average:28.127; most accessible tissue: Zhenshan97 panicle, score: 46.362	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0910687363	NA	5.09E-06	mr1008	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
vg0910687363	9.15E-06	3.99E-06	mr1009	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
vg0910687363	4.01E-06	4.01E-06	mr1778	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