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Detailed information for vg0804127081:

Variant ID: vg0804127081 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 4127081
Reference Allele: C	Alternative Allele: G
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGGCTTAAAAATTTTGTCTCGCGAATTAGCTTTCATTTATATAATTAGTTTTGTAAGTAGTATATATTTAATACTCTAAATTAGTGTCTACTCCCTGGAT[C/G]
CAAACACCACCTTACTTTCATCACGATCGTCCAAAATCTTCACGGTCTGGATCTTGTGAAGATTGCATAGGGAATCCAAAAATGCAGATGTCTCATCCTG

Reverse complement sequence

CAGGATGAGACATCTGCATTTTTGGATTCCCTATGCAATCTTCACAAGATCCAGACCGTGAAGATTTTGGACGATCGTGATGAAAGTAAGGTGGTGTTTG[G/C]
ATCCAGGGAGTAGACACTAATTTAGAGTATTAAATATATACTACTTACAAAACTAATTATATAAATGAAAGCTAATTCGCGAGACAAAATTTTTAAGCCT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	78.80%	1.30%	1.33%	18.51%	NA
All Indica	2759	70.20%	0.10%	0.69%	29.07%	NA
All Japonica	1512	89.60%	3.90%	2.65%	3.84%	NA
Aus	269	98.50%	0.00%	0.37%	1.12%	NA
Indica I	595	49.90%	0.00%	0.50%	49.58%	NA
Indica II	465	91.80%	0.20%	0.65%	7.31%	NA
Indica III	913	66.30%	0.00%	0.66%	33.08%	NA
Indica Intermediate	786	77.20%	0.10%	0.89%	21.76%	NA
Temperate Japonica	767	92.20%	4.30%	3.52%	0.00%	NA
Tropical Japonica	504	87.30%	1.20%	0.20%	11.31%	NA
Japonica Intermediate	241	86.30%	8.30%	4.98%	0.41%	NA
VI/Aromatic	96	96.90%	0.00%	2.08%	1.04%	NA
Intermediate	90	85.60%	1.10%	1.11%	12.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0804127081	C -> G	LOC_Os08g07370.1	missense_variant ; p.Gly137Ala; MODERATE	nonsynonymous_codon ; G137A	Average:27.93; most accessible tissue: Minghui63 panicle, score: 56.842	unknown	unknown	DELETERIOUS	0.00
vg0804127081	C -> DEL	LOC_Os08g07370.1	N	frameshift_variant	Average:27.93; most accessible tissue: Minghui63 panicle, score: 56.842	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0804127081	3.20E-06	NA	mr1549	Jap_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