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Detailed information for vg0104863244:

Variant ID: vg0104863244 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 4863244
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.96, G: 0.04, others allele: 0.00, population size: 53. )

Flanking Sequence (100 bp) in Reference Genome:

CGGTGTCCCCCGGCCGGGCTCGGTACGGCTGGCCACGGGCGACGGCACGGAGCTGCCAAACCCGTGGAACATCGAACACCTTCGCCGCTTCTACCCCTGA[A/G]
AGGGGGGGTCGGGTGTCAGGTTTCTATCTCGGGCCAACCCCGCACCCCCCTCGGGTGTGCAGGGTTGGCCGGGGGCTACCACACATGCACATATATTCCT

Reverse complement sequence

AGGAATATATGTGCATGTGTGGTAGCCCCCGGCCAACCCTGCACACCCGAGGGGGGTGCGGGGTTGGCCCGAGATAGAAACCTGACACCCGACCCCCCCT[T/C]
TCAGGGGTAGAAGCGGCGAAGGTGTTCGATGTTCCACGGGTTTGGCAGCTCCGTGCCGTCGCCCGTGGCCAGCCGTACCGAGCCCGGCCGGGGGACACCG

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	12.80%	2.80%	8.93%	75.48%	NA
All Indica	2759	1.60%	3.20%	11.71%	83.47%	NA
All Japonica	1512	35.20%	0.50%	0.86%	63.49%	NA
Aus	269	0.00%	10.40%	5.95%	83.64%	NA
Indica I	595	0.80%	1.80%	18.32%	78.99%	NA
Indica II	465	3.00%	3.40%	6.45%	87.10%	NA
Indica III	913	2.00%	3.90%	9.75%	84.34%	NA
Indica Intermediate	786	1.00%	3.20%	12.09%	83.72%	NA
Temperate Japonica	767	59.20%	0.00%	0.26%	40.55%	NA
Tropical Japonica	504	2.60%	1.40%	1.59%	94.44%	NA
Japonica Intermediate	241	27.00%	0.00%	1.24%	71.78%	NA
VI/Aromatic	96	17.70%	4.20%	57.29%	20.83%	NA
Intermediate	90	14.40%	3.30%	16.67%	65.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0104863244	A -> G	LOC_Os01g09530.1	downstream_gene_variant ; 634.0bp to feature; MODIFIER	silent_mutation	Average:18.163; most accessible tissue: Minghui63 panicle, score: 50.413	N	N	N	N
vg0104863244	A -> G	LOC_Os01g09520.1	intron_variant ; MODIFIER	silent_mutation	Average:18.163; most accessible tissue: Minghui63 panicle, score: 50.413	N	N	N	N
vg0104863244	A -> DEL	N	N	silent_mutation	Average:18.163; most accessible tissue: Minghui63 panicle, score: 50.413	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0104863244	NA	9.70E-07	mr1057_2	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
vg0104863244	NA	1.52E-06	mr1363_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
vg0104863244	NA	8.26E-06	mr1577_2	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
vg0104863244	NA	2.14E-06	mr1840_2	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