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Detailed information for vg0513252496:

Variant ID: vg0513252496 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 13252496
Reference Allele: A	Alternative Allele: C
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGCTTCGGCCACTCTCAAAAAATAATGCACGCCCTCGATAAACTCTTTGGACCACCGGTCAGCGTACATCCATTGCCGATCCATCTACATGAAATGAAAA[A/C]
AAATCGTACATAAATAAATTTTCGTATAGTAATGACAGTCACACAATAATGATAAAATATAATTATAAAATAATCCAACAAACAATTCATATTAACAAAT

Reverse complement sequence

ATTTGTTAATATGAATTGTTTGTTGGATTATTTTATAATTATATTTTATCATTATTGTGTGACTGTCATTACTATACGAAAATTTATTTATGTACGATTT[T/G]
TTTTCATTTCATGTAGATGGATCGGCAATGGATGTACGCTGACCGGTGGTCCAAAGAGTTTATCGAGGGCGTGCATTATTTTTTGAGAGTGGCCGAAGCT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	89.40%	10.10%	0.47%	0.04%	NA
All Indica	2759	90.00%	9.20%	0.76%	0.07%	NA
All Japonica	1512	99.70%	0.30%	0.00%	0.00%	NA
Aus	269	21.90%	77.70%	0.37%	0.00%	NA
Indica I	595	99.50%	0.50%	0.00%	0.00%	NA
Indica II	465	98.90%	1.10%	0.00%	0.00%	NA
Indica III	913	80.00%	17.70%	2.08%	0.22%	NA
Indica Intermediate	786	89.10%	10.70%	0.25%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.20%	0.80%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	88.90%	11.10%	0.00%	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
vg0513252496	A -> DEL	N	N	silent_mutation	Average:27.444; most accessible tissue: Minghui63 flag leaf, score: 38.136	N	N	N	N
vg0513252496	A -> C	LOC_Os05g23210.1	upstream_gene_variant ; 3139.0bp to feature; MODIFIER	silent_mutation	Average:27.444; most accessible tissue: Minghui63 flag leaf, score: 38.136	N	N	N	N
vg0513252496	A -> C	LOC_Os05g23220.1	intron_variant ; MODIFIER	silent_mutation	Average:27.444; most accessible tissue: Minghui63 flag leaf, score: 38.136	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0513252496	1.15E-07	NA	mr1247_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