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Detailed information for vg0224889308:

Variant ID: vg0224889308 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 24889308
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GTATCAGCCCACGTGTATAGGGTTAGGTGGGCGCGCCTAACGGGCGCACCTAACGCCCACCTAACTGCATTTAAAGCGGTCTATGCAACCGCGCCATGCC[G/A]
CATTTAATGCGGCGTGCTGCGCATCTGACCGGTCTGTGACCGGTTGAATGACCGATGGGACGACGACTGTGTACCCCCGTCCTGTCAGTGTGTCAGGCGG

Reverse complement sequence

CCGCCTGACACACTGACAGGACGGGGGTACACAGTCGTCGTCCCATCGGTCATTCAACCGGTCACAGACCGGTCAGATGCGCAGCACGCCGCATTAAATG[C/T]
GGCATGGCGCGGTTGCATAGACCGCTTTAAATGCAGTTAGGTGGGCGTTAGGTGCGCCCGTTAGGCGCGCCCACCTAACCCTATACACGTGGGCTGATAC

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	70.20%	0.20%	0.40%	29.16%	NA
All Indica	2759	56.10%	0.10%	0.22%	43.57%	NA
All Japonica	1512	92.30%	0.50%	0.79%	6.48%	NA
Aus	269	84.40%	0.00%	0.37%	15.24%	NA
Indica I	595	41.00%	0.00%	0.17%	58.82%	NA
Indica II	465	47.30%	0.20%	0.43%	52.04%	NA
Indica III	913	69.30%	0.20%	0.22%	30.23%	NA
Indica Intermediate	786	57.40%	0.00%	0.13%	42.49%	NA
Temperate Japonica	767	95.40%	0.00%	0.65%	3.91%	NA
Tropical Japonica	504	91.70%	1.40%	1.19%	5.75%	NA
Japonica Intermediate	241	83.40%	0.00%	0.41%	16.18%	NA
VI/Aromatic	96	83.30%	0.00%	0.00%	16.67%	NA
Intermediate	90	76.70%	0.00%	0.00%	23.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0224889308	G -> A	LOC_Os02g41510-LOC_Os02g41520	intergenic_region ; MODIFIER	silent_mutation	Average:14.642; most accessible tissue: Minghui63 root, score: 25.504	N	N	N	N
vg0224889308	G -> DEL	N	N	silent_mutation	Average:14.642; most accessible tissue: Minghui63 root, score: 25.504	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0224889308	3.38E-06	NA	mr1667	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