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Detailed information for vg0900686640:

Variant ID: vg0900686640 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 686640
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.98, C: 0.02, others allele: 0.00, population size: 108. )

Flanking Sequence (100 bp) in Reference Genome:

TTGGTCATTCTCGTGCTGGGGCCTAGATATTCTCGGGCCATTCCCACGAGGACAGGGCGGCTACAGGTTCCTATTCGTGGCGATCGACAAATTCACTAAG[T/C]
GGATCAAAGCAGTACCCACGGGGGAAATCAAGGCCAACAACGCCATCAAATTCAGCAAGGGGATATTTTGTAGATACGGACTACCGCACCGCATCATAAC

Reverse complement sequence

GTTATGATGCGGTGCGGTAGTCCGTATCTACAAAATATCCCCTTGCTGAATTTGATGGCGTTGTTGGCCTTGATTTCCCCCGTGGGTACTGCTTTGATCC[A/G]
CTTAGTGAATTTGTCGATCGCCACGAATAGGAACCTGTAGCCGCCCTGTCCTCGTGGGAATGGCCCGAGAATATCTAGGCCCCAGCACGAGAATGACCAA

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	51.40%	35.20%	13.39%	0.06%	NA
All Indica	2759	22.20%	55.20%	22.54%	0.11%	NA
All Japonica	1512	99.10%	0.80%	0.13%	0.00%	NA
Aus	269	88.80%	10.40%	0.74%	0.00%	NA
Indica I	595	11.10%	63.50%	25.38%	0.00%	NA
Indica II	465	22.40%	60.60%	16.99%	0.00%	NA
Indica III	913	24.60%	47.90%	27.27%	0.22%	NA
Indica Intermediate	786	27.60%	54.10%	18.19%	0.13%	NA
Temperate Japonica	767	99.30%	0.50%	0.13%	0.00%	NA
Tropical Japonica	504	99.00%	1.00%	0.00%	0.00%	NA
Japonica Intermediate	241	98.30%	1.20%	0.41%	0.00%	NA
VI/Aromatic	96	29.20%	69.80%	1.04%	0.00%	NA
Intermediate	90	56.70%	36.70%	6.67%	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
vg0900686640	T -> DEL	LOC_Os09g01980.1	N	frameshift_variant	Average:38.07; most accessible tissue: Zhenshan97 flag leaf, score: 72.012	N	N	N	N
vg0900686640	T -> C	LOC_Os09g01980.1	missense_variant ; p.Trp1066Arg; MODERATE	nonsynonymous_codon ; W1066R	Average:38.07; most accessible tissue: Zhenshan97 flag leaf, score: 72.012	benign	1.049	DELETERIOUS	0.01

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0900686640	1.87E-06	1.87E-06	mr1581	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
vg0900686640	NA	4.47E-07	mr1728	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