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Detailed information for vg0527033385:

Variant ID: vg0527033385 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 27033385
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.93, T: 0.06, others allele: 0.00, population size: 92. )

Flanking Sequence (100 bp) in Reference Genome:

GATGGCGGCGCATGGACGAGCAGCGGCGCACGGCGACGAACACGACGCCGAGGTGGCATGGTGCCGCCGCGGGCGCGCCGGGGAAGGGGACGGAGGCGTG[C/T]
GGGAACGGCGTCCTTGGTCGCGGCGGTGGCGTTCTTGGCCGTGACGACGAAGGAGGCGGCGGTGCTCTGGGTTGGCCGCGCGACGGCGACCGGGGTCGAG

Reverse complement sequence

CTCGACCCCGGTCGCCGTCGCGCGGCCAACCCAGAGCACCGCCGCCTCCTTCGTCGTCACGGCCAAGAACGCCACCGCCGCGACCAAGGACGCCGTTCCC[G/A]
CACGCCTCCGTCCCCTTCCCCGGCGCGCCCGCGGCGGCACCATGCCACCTCGGCGTCGTGTTCGTCGCCGTGCGCCGCTGCTCGTCCATGCGCCGCCATC

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	65.10%	29.50%	5.04%	0.38%	NA
All Indica	2759	44.50%	47.70%	7.25%	0.54%	NA
All Japonica	1512	98.50%	0.10%	1.26%	0.13%	NA
Aus	269	79.60%	17.10%	2.97%	0.37%	NA
Indica I	595	39.80%	53.80%	6.22%	0.17%	NA
Indica II	465	71.80%	22.20%	6.02%	0.00%	NA
Indica III	913	27.40%	63.50%	8.00%	1.10%	NA
Indica Intermediate	786	51.80%	39.80%	7.89%	0.51%	NA
Temperate Japonica	767	99.90%	0.00%	0.13%	0.00%	NA
Tropical Japonica	504	96.60%	0.20%	2.78%	0.40%	NA
Japonica Intermediate	241	98.30%	0.00%	1.66%	0.00%	NA
VI/Aromatic	96	82.30%	11.50%	6.25%	0.00%	NA
Intermediate	90	72.20%	22.20%	5.56%	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
vg0527033385	C -> T	LOC_Os05g46700.1	missense_variant ; p.Ala152Val; MODERATE	nonsynonymous_codon ; A152V	Average:78.758; most accessible tissue: Zhenshan97 panicle, score: 90.061	unknown	unknown	TOLERATED	0.12
vg0527033385	C -> DEL	LOC_Os05g46700.1	N	frameshift_variant	Average:78.758; most accessible tissue: Zhenshan97 panicle, score: 90.061	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0527033385	NA	3.26E-06	mr1528	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
vg0527033385	6.80E-06	NA	mr1633	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