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Detailed information for vg0805895531:

Variant ID: vg0805895531 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 5895531
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CCGAACGACGCCGACTGGGGGAGGAGCGTCAAGCACAGGAACAAGAACGGCTGCGGCGTGAGCAACAGGAGCGCGAGCGGGCCGCTGAGGCTGAAGACCG[A/G]
CGGCAACGAGCCTTGGATGCAGGGCGCCGAGCGCGAGATCTTATTGGCCAGCAAGATGTTGAGGGAACACCGGTTTTCCGCACCCCACAACAGAACGCTG

Reverse complement sequence

CAGCGTTCTGTTGTGGGGTGCGGAAAACCGGTGTTCCCTCAACATCTTGCTGGCCAATAAGATCTCGCGCTCGGCGCCCTGCATCCAAGGCTCGTTGCCG[T/C]
CGGTCTTCAGCCTCAGCGGCCCGCTCGCGCTCCTGTTGCTCACGCCGCAGCCGTTCTTGTTCCTGTGCTTGACGCTCCTCCCCCAGTCGGCGTCGTTCGG

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	96.40%	2.20%	1.46%	0.00%	NA
All Indica	2759	96.10%	2.60%	1.30%	0.00%	NA
All Japonica	1512	99.80%	0.10%	0.13%	0.00%	NA
Aus	269	80.30%	10.00%	9.67%	0.00%	NA
Indica I	595	93.60%	3.40%	3.03%	0.00%	NA
Indica II	465	99.60%	0.20%	0.22%	0.00%	NA
Indica III	913	95.50%	3.50%	0.99%	0.00%	NA
Indica Intermediate	786	96.70%	2.30%	1.02%	0.00%	NA
Temperate Japonica	767	99.90%	0.00%	0.13%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.40%	0.41%	0.00%	NA
VI/Aromatic	96	94.80%	1.00%	4.17%	0.00%	NA
Intermediate	90	96.70%	2.20%	1.11%	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
vg0805895531	A -> G	LOC_Os08g10160.1	synonymous_variant ; p.Arg183Arg; LOW	synonymous_codon	Average:39.512; most accessible tissue: Minghui63 young leaf, score: 61.887	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0805895531	3.84E-06	3.84E-06	mr1282_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