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Detailed information for vg0334098591:

Variant ID: vg0334098591 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 34098591
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.93, T: 0.07, others allele: 0.00, population size: 295. )

Flanking Sequence (100 bp) in Reference Genome:

TGATTTTGATCAGCTTACGTCTAACCGTGTTCGGTGGACTCCCTACACTCAGCACGATGACAATGATCGTGCACCACTCGGTCTCATGAACCTTTGCATG[C/T]
GAGATATGCAACTCTGGAGGACTACTTGTCACCTCGTGATGGATATGCACGTCGAGCCACACAATGTCCATAGGGTTATGAAATAATTGGGCATGTATCA

Reverse complement sequence

TGATACATGCCCAATTATTTCATAACCCTATGGACATTGTGTGGCTCGACGTGCATATCCATCACGAGGTGACAAGTAGTCCTCCAGAGTTGCATATCTC[G/A]
CATGCAAAGGTTCATGAGACCGAGTGGTGCACGATCATTGTCATCGTGCTGAGTGTAGGGAGTCCACCGAACACGGTTAGACGTAAGCTGATCAAAATCA

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	59.90%	39.70%	0.08%	0.36%	NA
All Indica	2759	41.20%	58.20%	0.11%	0.43%	NA
All Japonica	1512	98.10%	1.70%	0.00%	0.13%	NA
Aus	269	20.80%	79.20%	0.00%	0.00%	NA
Indica I	595	33.60%	66.20%	0.17%	0.00%	NA
Indica II	465	22.80%	76.30%	0.22%	0.65%	NA
Indica III	913	54.50%	45.20%	0.00%	0.22%	NA
Indica Intermediate	786	42.40%	56.60%	0.13%	0.89%	NA
Temperate Japonica	767	99.50%	0.40%	0.00%	0.13%	NA
Tropical Japonica	504	95.40%	4.40%	0.00%	0.20%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	97.90%	1.00%	0.00%	1.04%	NA
Intermediate	90	65.60%	31.10%	1.11%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0334098591	C -> T	LOC_Os03g59910.1	stop_gained ; p.Arg74*; HIGH	stop_gained	Average:45.694; most accessible tissue: Zhenshan97 young leaf, score: 55.261	N	N	N	N
vg0334098591	C -> DEL	LOC_Os03g59910.1	N	frameshift_variant	Average:45.694; most accessible tissue: Zhenshan97 young leaf, score: 55.261	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0334098591	NA	6.11E-07	mr1586	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