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Detailed information for vg0316348941:

Variant ID: vg0316348941 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 16348941
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 241. )

Flanking Sequence (100 bp) in Reference Genome:

AGTGGCTGGCGAATCCAGTGTTGGTGCGGAAGTCAAATGGCAAATGGCGCATGTGTGTCGATTTCACAAACTTAAACAAAGCATGTCCGAAGGATGATTT[C/T]
CCCTTGCCACGGATCGACCAGCTCGTGGATTCGACAGCCGGCTGTGAACTCATGAGCTTCCTAGATGCATATTCCGGCTATCATCAGATTCGCATGAACC

Reverse complement sequence

GGTTCATGCGAATCTGATGATAGCCGGAATATGCATCTAGGAAGCTCATGAGTTCACAGCCGGCTGTCGAATCCACGAGCTGGTCGATCCGTGGCAAGGG[G/A]
AAATCATCCTTCGGACATGCTTTGTTTAAGTTTGTGAAATCGACACACATGCGCCATTTGCCATTTGACTTCCGCACCAACACTGGATTCGCCAGCCACT

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	49.90%	46.40%	0.34%	3.34%	NA
All Indica	2759	77.20%	21.10%	0.40%	1.30%	NA
All Japonica	1512	1.20%	91.30%	0.13%	7.41%	NA
Aus	269	60.60%	36.40%	0.37%	2.60%	NA
Indica I	595	58.20%	39.80%	0.50%	1.51%	NA
Indica II	465	92.30%	7.50%	0.22%	0.00%	NA
Indica III	913	83.20%	15.10%	0.33%	1.31%	NA
Indica Intermediate	786	75.80%	21.80%	0.51%	1.91%	NA
Temperate Japonica	767	0.70%	97.30%	0.13%	1.96%	NA
Tropical Japonica	504	2.40%	86.10%	0.00%	11.51%	NA
Japonica Intermediate	241	0.40%	83.00%	0.41%	16.18%	NA
VI/Aromatic	96	9.40%	87.50%	1.04%	2.08%	NA
Intermediate	90	42.20%	55.60%	1.11%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0316348941	C -> T	LOC_Os03g28370.1	synonymous_variant ; p.Phe682Phe; LOW	synonymous_codon	Average:46.807; most accessible tissue: Zhenshan97 root, score: 63.237	N	N	N	N
vg0316348941	C -> DEL	LOC_Os03g28370.1	N	frameshift_variant	Average:46.807; most accessible tissue: Zhenshan97 root, score: 63.237	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0316348941	NA	2.18E-09	mr1191	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
vg0316348941	NA	9.87E-07	mr1408	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
vg0316348941	NA	3.31E-09	mr1644	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
vg0316348941	NA	1.54E-06	mr1020_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
vg0316348941	NA	1.31E-07	mr1749_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