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Detailed information for vg0817248882:

Variant ID: vg0817248882 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 17248882
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CGGGGTGTCCCATAATTTCATGCTCAATTGGGACACAACACTTCGATCAGGCCCAATGTGATCTTGAGGCCAGTGTCAGCGTGATGCCGAAGGACGCCTT[C/T]
GACAAGCTGAACTATACGGGGTTGATTCCAACACCGATGAGGCTCCAACTGGCTGACTCCTCTGTCTGCTATCCAGTGGGCATCGCCGAGGATGTGCCAA

Reverse complement sequence

TTGGCACATCCTCGGCGATGCCCACTGGATAGCAGACAGAGGAGTCAGCCAGTTGGAGCCTCATCGGTGTTGGAATCAACCCCGTATAGTTCAGCTTGTC[G/A]
AAGGCGTCCTTCGGCATCACGCTGACACTGGCCTCAAGATCACATTGGGCCTGATCGAAGTGTTGTGTCCCAATTGAGCATGAAATTATGGGACACCCCG

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	37.90%	31.70%	2.75%	27.70%	NA
All Indica	2759	43.90%	12.10%	3.70%	40.30%	NA
All Japonica	1512	29.60%	64.10%	0.33%	6.02%	NA
Aus	269	8.20%	56.10%	7.43%	28.25%	NA
Indica I	595	57.50%	6.70%	4.37%	31.43%	NA
Indica II	465	69.20%	4.70%	1.51%	24.52%	NA
Indica III	913	22.20%	21.60%	4.05%	52.14%	NA
Indica Intermediate	786	43.60%	9.70%	4.07%	42.62%	NA
Temperate Japonica	767	28.30%	70.90%	0.00%	0.78%	NA
Tropical Japonica	504	20.60%	63.70%	0.60%	15.08%	NA
Japonica Intermediate	241	52.30%	43.20%	0.83%	3.73%	NA
VI/Aromatic	96	86.50%	4.20%	1.04%	8.33%	NA
Intermediate	90	32.20%	41.10%	2.22%	24.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0817248882	C -> T	LOC_Os08g28260.1	synonymous_variant ; p.Phe443Phe; LOW	synonymous_codon	Average:31.965; most accessible tissue: Minghui63 panicle, score: 46.754	N	N	N	N
vg0817248882	C -> DEL	LOC_Os08g28260.1	N	frameshift_variant	Average:31.965; most accessible tissue: Minghui63 panicle, score: 46.754	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0817248882	3.62E-07	NA	mr1746	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
vg0817248882	2.31E-06	2.64E-06	mr1746	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