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Detailed information for vg0817164286:

Variant ID: vg0817164286 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 17164286
Reference Allele: C	Alternative Allele: T,A
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACCAGGAAGATCCAACCTGGCCAGAGTACGTCTCTCGACGAGATTGGAGTTATCGTCATCAACTATTTGATTCGGCGAGATCGATCAAGCTCCAAGATAT[C/T,A]
ATCGCCGCGAAGGATAATTGTTCAATATCGCCAGATACGAGACTTCGGTTCATGTCGACTACAACGGAACTTGCCGATCTACGATCATAATTGGTCCCGA

Reverse complement sequence

TCGGGACCAATTATGATCGTAGATCGGCAAGTTCCGTTGTAGTCGACATGAACCGAAGTCTCGTATCTGGCGATATTGAACAATTATCCTTCGCGGCGAT[G/A,T]
ATATCTTGGAGCTTGATCGATCTCGCCGAATCAAATAGTTGATGACGATAACTCCAATCTCGTCGAGAGACGTACTCTGGCCAGGTTGGATCTTCCTGGT

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	82.20%	15.90%	0.15%	1.48%	A: 0.19%
All Indica	2759	98.60%	1.00%	0.04%	0.00%	A: 0.33%
All Japonica	1512	54.50%	40.70%	0.33%	4.43%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	99.80%	0.20%	0.00%	0.00%	NA
Indica II	465	97.00%	3.00%	0.00%	0.00%	NA
Indica III	913	98.80%	0.20%	0.00%	0.00%	A: 0.99%
Indica Intermediate	786	98.50%	1.40%	0.13%	0.00%	NA
Temperate Japonica	767	69.10%	30.50%	0.39%	0.00%	NA
Tropical Japonica	504	39.10%	47.80%	0.40%	12.70%	NA
Japonica Intermediate	241	40.20%	58.50%	0.00%	1.24%	NA
VI/Aromatic	96	10.40%	89.60%	0.00%	0.00%	NA
Intermediate	90	71.10%	24.40%	1.11%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0817164286	C -> T	LOC_Os08g28130.1	intron_variant ; MODIFIER	silent_mutation	Average:43.658; most accessible tissue: Zhenshan97 flower, score: 59.202	N	N	N	N
vg0817164286	C -> A	LOC_Os08g28130.1	intron_variant ; MODIFIER	silent_mutation	Average:43.658; most accessible tissue: Zhenshan97 flower, score: 59.202	N	N	N	N
vg0817164286	C -> DEL	N	N	silent_mutation	Average:43.658; most accessible tissue: Zhenshan97 flower, score: 59.202	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0817164286	7.58E-07	NA	mr1006	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
vg0817164286	9.75E-07	NA	mr1007	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
vg0817164286	8.66E-07	NA	mr1052	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
vg0817164286	1.68E-07	NA	mr1301	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
vg0817164286	5.23E-06	NA	mr1410	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
vg0817164286	2.27E-06	NA	mr1301_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
vg0817164286	NA	2.83E-09	mr1398_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
vg0817164286	3.19E-06	NA	mr1410_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
vg0817164286	8.37E-06	NA	mr1993_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