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Detailed information for vg0527033218:

Variant ID: vg0527033218 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 27033218
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.93, A: 0.07, others allele: 0.00, population size: 96. )

Flanking Sequence (100 bp) in Reference Genome:

CGAAGCTCGCCGCGGCTGCTCGCGCGAGCAGCGCCAAGCGGCGGTGGCGAGAGCTACACGATGCGGAAAAGGAAAGGGGGTGCCAAGGGGAGGGAGGAGC[C/A]
GAGGAGCTCACCGTCGAGCGGGGAACGGCGTCGCCGGACTTCGGTGATGGGAAGGGGAGGAAGGCCGATGGCGGCGCATGGACGAGCAGCGGCGCACGGC

Reverse complement sequence

GCCGTGCGCCGCTGCTCGTCCATGCGCCGCCATCGGCCTTCCTCCCCTTCCCATCACCGAAGTCCGGCGACGCCGTTCCCCGCTCGACGGTGAGCTCCTC[G/T]
GCTCCTCCCTCCCCTTGGCACCCCCTTTCCTTTTCCGCATCGTGTAGCTCTCGCCACCGCCGCTTGGCGCTGCTCGCGCGAGCAGCCGCGGCGAGCTTCG

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	67.10%	24.20%	7.72%	1.02%	NA
All Indica	2759	47.40%	39.20%	12.03%	1.38%	NA
All Japonica	1512	98.50%	0.10%	0.79%	0.60%	NA
Aus	269	80.70%	14.50%	4.46%	0.37%	NA
Indica I	595	40.30%	43.20%	15.29%	1.18%	NA
Indica II	465	73.30%	16.60%	8.82%	1.29%	NA
Indica III	913	32.40%	55.50%	10.08%	1.97%	NA
Indica Intermediate	786	54.70%	30.70%	13.74%	0.89%	NA
Temperate Japonica	767	99.70%	0.00%	0.26%	0.00%	NA
Tropical Japonica	504	96.60%	0.20%	1.79%	1.39%	NA
Japonica Intermediate	241	98.80%	0.00%	0.41%	0.83%	NA
VI/Aromatic	96	89.60%	7.30%	3.12%	0.00%	NA
Intermediate	90	76.70%	16.70%	6.67%	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
vg0527033218	C -> DEL	LOC_Os05g46700.1	N	frameshift_variant	Average:79.303; most accessible tissue: Zhenshan97 flag leaf, score: 90.181	N	N	N	N
vg0527033218	C -> A	LOC_Os05g46700.1	synonymous_variant ; p.Ala96Ala; LOW	synonymous_codon	Average:79.303; most accessible tissue: Zhenshan97 flag leaf, score: 90.181	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0527033218	4.73E-06	NA	mr1877_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