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Detailed information for vg0404085755:

Variant ID: vg0404085755 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 4085755
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 112. )

Flanking Sequence (100 bp) in Reference Genome:

AAAAGCTCGCAGGCCAAATTGCGGCGCTCAGTCGATTCCTCTCAAAGGCAGCCGAAAGAGGTTTGCCCTTCTTCAAGACCCTCCGGGGCGCGGGAAAGTT[T/C]
AGCTGGACACCCGAATGCCAAGCAGCGTTCGACGAGGTAAAGCAATATCCGCAAAGCCCACCCACTTTGGTCAGCCCAGCACTGGGAAGCGAACTGCTGC

Reverse complement sequence

GCAGCAGTTCGCTTCCCAGTGCTGGGCTGACCAAAGTGGGTGGGCTTTGCGGATATTGCTTTACCTCGTCGAACGCTGCTTGGCATTCGGGTGTCCAGCT[A/G]
AACTTTCCCGCGCCCCGGAGGGTCTTGAAGAAGGGCAAACCTCTTTCGGCTGCCTTTGAGAGGAATCGACTGAGCGCCGCAATTTGGCCTGCGAGCTTTT

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	90.10%	0.30%	0.78%	8.80%	NA
All Indica	2759	86.80%	0.30%	1.16%	11.67%	NA
All Japonica	1512	94.20%	0.00%	0.26%	5.49%	NA
Aus	269	94.40%	2.20%	0.37%	2.97%	NA
Indica I	595	76.80%	0.70%	2.86%	19.66%	NA
Indica II	465	90.10%	0.40%	1.08%	8.39%	NA
Indica III	913	91.90%	0.10%	0.22%	7.78%	NA
Indica Intermediate	786	86.60%	0.30%	1.02%	12.09%	NA
Temperate Japonica	767	99.30%	0.00%	0.00%	0.65%	NA
Tropical Japonica	504	88.50%	0.00%	0.60%	10.91%	NA
Japonica Intermediate	241	90.00%	0.00%	0.41%	9.54%	NA
VI/Aromatic	96	97.90%	0.00%	0.00%	2.08%	NA
Intermediate	90	98.90%	0.00%	0.00%	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
vg0404085755	T -> C	LOC_Os04g07670.1	synonymous_variant ; p.Phe788Phe; LOW	synonymous_codon	Average:46.767; most accessible tissue: Minghui63 young leaf, score: 74.007	N	N	N	N
vg0404085755	T -> DEL	LOC_Os04g07670.1	N	frameshift_variant	Average:46.767; most accessible tissue: Minghui63 young leaf, score: 74.007	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0404085755	1.21E-07	1.21E-07	mr1412	Ind_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