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Detailed information for vg0623330404:

Variant ID: vg0623330404 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 23330404
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CTCGATCTTTGTTATCATGACGCCGTGAAGAGACATGACGCCGGGAACGGTTCTCGTTGTCTTGTGTGCGTCGTGCCTCTCGGCTGCCGTTGAGGTGATC[A/G]
CGGAGATCGCCGGTGCCGCGAGGTGGAGGGGTGGCTCGTTGAGGCGATTCCCTCCGTTCAGGGTTTTCACCATTGGCATCGCCAGTTGGTGGCTGCTCTG

Reverse complement sequence

CAGAGCAGCCACCAACTGGCGATGCCAATGGTGAAAACCCTGAACGGAGGGAATCGCCTCAACGAGCCACCCCTCCACCTCGCGGCACCGGCGATCTCCG[T/C]
GATCACCTCAACGGCAGCCGAGAGGCACGACGCACACAAGACAACGAGAACCGTTCCCGGCGTCATGTCTCTTCACGGCGTCATGATAACAAAGATCGAG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	92.20%	7.60%	0.25%	0.00%	NA
All Indica	2759	99.70%	0.10%	0.11%	0.00%	NA
All Japonica	1512	76.30%	23.10%	0.60%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.10%	0.60%	0.22%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.60%	0.10%	0.25%	0.00%	NA
Temperate Japonica	767	59.10%	40.20%	0.78%	0.00%	NA
Tropical Japonica	504	98.80%	0.80%	0.40%	0.00%	NA
Japonica Intermediate	241	84.20%	15.40%	0.41%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	94.40%	5.60%	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
vg0623330404	A -> G	LOC_Os06g39320.1	missense_variant ; p.Val27Ala; MODERATE	nonsynonymous_codon ; V27A	Average:53.288; most accessible tissue: Zhenshan97 flag leaf, score: 71.238	unknown	unknown	TOLERATED	0.97

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0623330404	NA	2.18E-06	mr1880	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0623330404	6.97E-07	8.75E-09	mr1910	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
vg0623330404	9.01E-06	9.01E-06	mr1910	Jap_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0623330404	NA	3.70E-07	mr1977	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251