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Detailed information for vg0907789558:

Variant ID: vg0907789558 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 7789558
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.68, C: 0.32, others allele: 0.00, population size: 72. )

Flanking Sequence (100 bp) in Reference Genome:

TAAAACCGACATCTATGAAGCTTTTTTCACCTTTTTACAATATAAAAGTAAGAACTGGTACATATAATCACTCATTGGCACTGGTTTATAACAAAACTGA[C/T]
ATAATTAATCCCCCAAATCATAGGTGTTGATTCTTTTTATAAACCGGTACCTGTAGACATCACACAGGTGCTGGTTCTTATAATAAACTGGCACATACAA

Reverse complement sequence

TTGTATGTGCCAGTTTATTATAAGAACCAGCACCTGTGTGATGTCTACAGGTACCGGTTTATAAAAAGAATCAACACCTATGATTTGGGGGATTAATTAT[G/A]
TCAGTTTTGTTATAAACCAGTGCCAATGAGTGATTATATGTACCAGTTCTTACTTTTATATTGTAAAAAGGTGAAAAAAGCTTCATAGATGTCGGTTTTA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	86.50%	13.10%	0.02%	0.40%	NA
All Indica	2759	98.60%	1.40%	0.00%	0.00%	NA
All Japonica	1512	65.30%	33.40%	0.07%	1.26%	NA
Aus	269	78.80%	21.20%	0.00%	0.00%	NA
Indica I	595	99.70%	0.30%	0.00%	0.00%	NA
Indica II	465	99.80%	0.20%	0.00%	0.00%	NA
Indica III	913	97.80%	2.20%	0.00%	0.00%	NA
Indica Intermediate	786	98.00%	2.00%	0.00%	0.00%	NA
Temperate Japonica	767	38.60%	61.30%	0.00%	0.13%	NA
Tropical Japonica	504	95.80%	0.40%	0.20%	3.57%	NA
Japonica Intermediate	241	86.30%	13.70%	0.00%	0.00%	NA
VI/Aromatic	96	96.90%	3.10%	0.00%	0.00%	NA
Intermediate	90	85.60%	14.40%	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
vg0907789558	C -> DEL	N	N	silent_mutation	Average:63.867; most accessible tissue: Callus, score: 80.708	N	N	N	N
vg0907789558	C -> T	LOC_Os09g13460-LOC_Os09g13470	intergenic_region ; MODIFIER	silent_mutation	Average:63.867; most accessible tissue: Callus, score: 80.708	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0907789558	4.09E-06	3.63E-20	mr1010_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
vg0907789558	2.37E-06	1.51E-12	mr1010_2	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
vg0907789558	NA	1.93E-07	mr1013_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
vg0907789558	NA	3.20E-06	mr1330_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