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Detailed information for vg0519405460:

Variant ID: vg0519405460 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 19405460
Reference Allele: A	Alternative Allele: C
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GACTCTCCCAACGCCCACTCCTTCACCTCTTCCCCCGGTTTTCCCTAAAAATCGGTGCTGTTTTGACCCCCACCATGAGCCCACGTCTACACCCCACTCC[A/C]
CCGGCCATTGCCGCCCTTCTCCGAACTCCTCGCACCTCCCGGGCATATATAAAGCTTCATCATGCTCCACTCTCTAGAGGGAGGTAAGCTCAATGCGCGA

Reverse complement sequence

TCGCGCATTGAGCTTACCTCCCTCTAGAGAGTGGAGCATGATGAAGCTTTATATATGCCCGGGAGGTGCGAGGAGTTCGGAGAAGGGCGGCAATGGCCGG[T/G]
GGAGTGGGGTGTAGACGTGGGCTCATGGTGGGGGTCAAAACAGCACCGATTTTTAGGGAAAACCGGGGGAAGAGGTGAAGGAGTGGGCGTTGGGAGAGTC

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	99.60%	0.40%	0.04%	0.00%	NA
All Indica	2759	99.50%	0.40%	0.07%	0.00%	NA
All Japonica	1512	99.90%	0.10%	0.00%	0.00%	NA
Aus	269	98.90%	1.10%	0.00%	0.00%	NA
Indica I	595	99.70%	0.30%	0.00%	0.00%	NA
Indica II	465	99.40%	0.60%	0.00%	0.00%	NA
Indica III	913	99.20%	0.70%	0.11%	0.00%	NA
Indica Intermediate	786	99.70%	0.10%	0.13%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	98.90%	1.10%	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
vg0519405460	A -> C	LOC_Os05g33090.1	synonymous_variant ; p.Pro52Pro; LOW	N	Average:80.953; most accessible tissue: Minghui63 flag leaf, score: 99.613	N	N	N	N
vg0519405460	A -> C	LOC_Os05g33100.1	upstream_gene_variant ; 4124.0bp to feature; MODIFIER	N	Average:80.953; most accessible tissue: Minghui63 flag leaf, score: 99.613	N	N	N	N
vg0519405460	A -> C	LOC_Os05g33080.1	downstream_gene_variant ; 1904.0bp to feature; MODIFIER	N	Average:80.953; most accessible tissue: Minghui63 flag leaf, score: 99.613	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0519405460	2.51E-07	2.28E-07	mr1910_2	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