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Detailed information for vg0708797466:

Variant ID: vg0708797466 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 8797466
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CTTTAAGAGATGGCAGATCAGGGTCACTCTGTGGCTGACAGCTATGAAATGCTTCTGGGTGAGTACTGGCAAGCCTATGGGCGTTCTTAATGTTGATCAG[C/T]
AGAAAGAATTCGATGAGGCCACTACTCTCTTTGTGGGATGCATTCTTAGCATGCTTGGCGATCGTCTGGTCGAGGTGTATATGCATATGACCGACGCTAA

Reverse complement sequence

TTAGCGTCGGTCATATGCATATACACCTCGACCAGACGATCGCCAAGCATGCTAAGAATGCATCCCACAAAGAGAGTAGTGGCCTCATCGAATTCTTTCT[G/A]
CTGATCAACATTAAGAACGCCCATAGGCTTGCCAGTACTCACCCAGAAGCATTTCATAGCTGTCAGCCACAGAGTGACCCTGATCTGCCATCTCTTAAAG

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	84.10%	15.40%	0.44%	0.00%	NA
All Indica	2759	73.40%	26.10%	0.43%	0.00%	NA
All Japonica	1512	99.90%	0.10%	0.07%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	23.20%	76.50%	0.34%	0.00%	NA
Indica II	465	88.40%	11.40%	0.22%	0.00%	NA
Indica III	913	99.00%	0.50%	0.44%	0.00%	NA
Indica Intermediate	786	72.90%	26.50%	0.64%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.00%	0.41%	0.00%	NA
VI/Aromatic	96	92.70%	0.00%	7.29%	0.00%	NA
Intermediate	90	91.10%	7.80%	1.11%	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
vg0708797466	C -> T	LOC_Os07g15260.1	stop_gained ; p.Gln51*; HIGH	stop_gained	Average:21.255; most accessible tissue: Minghui63 panicle, score: 38.588	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0708797466	NA	5.35E-06	mr1170	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
vg0708797466	NA	1.89E-06	mr1439_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
vg0708797466	4.37E-06	4.64E-06	mr1616_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
vg0708797466	NA	5.73E-06	mr1968_2	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