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Detailed information for vg0805024504:

Variant ID: vg0805024504 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 5024504
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATAGTTTACATCGTGTACACAACAATTACGGCAATACATCGGCGGTGACGGTTGACCACACGTACTTTCTCCTCACTATTGTTCCTTCCTTGTGATCGCT[A/G]
CGTAAGGGGTGTCTTCATTTGATAGGAGGATGCTAGGGTCAATCGTCACCGTGAAAGGGGGTTGCCCATCAAACTGATCGTAATCCTCGTCAGTCTTGTC

Reverse complement sequence

GACAAGACTGACGAGGATTACGATCAGTTTGATGGGCAACCCCCTTTCACGGTGACGATTGACCCTAGCATCCTCCTATCAAATGAAGACACCCCTTACG[T/C]
AGCGATCACAAGGAAGGAACAATAGTGAGGAGAAAGTACGTGTGGTCAACCGTCACCGCCGATGTATTGCCGTAATTGTTGTGTACACGATGTAAACTAT

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	71.30%	0.20%	11.83%	16.67%	NA
All Indica	2759	67.10%	0.00%	13.88%	18.99%	NA
All Japonica	1512	77.60%	0.50%	6.88%	15.01%	NA
Aus	269	80.30%	0.40%	15.61%	3.72%	NA
Indica I	595	95.50%	0.00%	0.67%	3.87%	NA
Indica II	465	55.10%	0.00%	12.04%	32.90%	NA
Indica III	913	51.40%	0.00%	23.88%	24.75%	NA
Indica Intermediate	786	71.10%	0.00%	13.36%	15.52%	NA
Temperate Japonica	767	91.80%	0.10%	1.43%	6.65%	NA
Tropical Japonica	504	54.20%	1.00%	15.28%	29.56%	NA
Japonica Intermediate	241	81.30%	0.80%	6.64%	11.20%	NA
VI/Aromatic	96	68.80%	0.00%	18.75%	12.50%	NA
Intermediate	90	70.00%	0.00%	13.33%	16.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0805024504	A -> G	LOC_Os08g08680.1	missense_variant ; p.Val574Ala; MODERATE	nonsynonymous_codon ; V574A	Average:16.139; most accessible tissue: Zhenshan97 flag leaf, score: 31.305	unknown	unknown	DELETERIOUS	0.00
vg0805024504	A -> DEL	LOC_Os08g08680.1	N	frameshift_variant	Average:16.139; most accessible tissue: Zhenshan97 flag leaf, score: 31.305	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0805024504	2.72E-07	5.74E-06	mr1113_2	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