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Detailed information for vg0118939890:

Variant ID: vg0118939890 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 18939890
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.80, A: 0.18, others allele: 0.00, population size: 49. )

Flanking Sequence (100 bp) in Reference Genome:

TTATGAATACGGAGGGAGTATATACAAGACTTGATCAGAGATACGAGATCATCATTAACAACGAGTGGGCAATGAGAAGCATTCCAGTCACTTCACTTTG[A/G]
CTGTGTTTAGTTCGGCCTAAAGTTTAGAATTTAGTTGAAATTGGAGACGATGTGACTGAAAAGTTGTGTGTGTATGAAAGATTTGATGTGATAGAAAGTT

Reverse complement sequence

AACTTTCTATCACATCAAATCTTTCATACACACACAACTTTTCAGTCACATCGTCTCCAATTTCAACTAAATTCTAAACTTTAGGCCGAACTAAACACAG[T/C]
CAAAGTGAAGTGACTGGAATGCTTCTCATTGCCCACTCGTTGTTAATGATGATCTCGTATCTCTGATCAAGTCTTGTATATACTCCCTCCGTATTCATAA

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	74.70%	23.10%	0.85%	1.33%	NA
All Indica	2759	93.00%	3.70%	1.01%	2.28%	NA
All Japonica	1512	44.80%	54.60%	0.66%	0.00%	NA
Aus	269	75.10%	24.50%	0.37%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	85.40%	2.60%	1.72%	10.32%	NA
Indica III	913	92.70%	6.90%	0.22%	0.22%	NA
Indica Intermediate	786	92.50%	3.60%	2.29%	1.65%	NA
Temperate Japonica	767	15.30%	83.60%	1.17%	0.00%	NA
Tropical Japonica	504	79.60%	20.20%	0.20%	0.00%	NA
Japonica Intermediate	241	66.00%	34.00%	0.00%	0.00%	NA
VI/Aromatic	96	30.20%	69.80%	0.00%	0.00%	NA
Intermediate	90	62.20%	36.70%	1.11%	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
vg0118939890	A -> G	LOC_Os01g34330.1	downstream_gene_variant ; 611.0bp to feature; MODIFIER	silent_mutation	Average:63.286; most accessible tissue: Minghui63 panicle, score: 75.788	N	N	N	N
vg0118939890	A -> G	LOC_Os01g34350.1	downstream_gene_variant ; 498.0bp to feature; MODIFIER	silent_mutation	Average:63.286; most accessible tissue: Minghui63 panicle, score: 75.788	N	N	N	N
vg0118939890	A -> G	LOC_Os01g34330.2	downstream_gene_variant ; 611.0bp to feature; MODIFIER	silent_mutation	Average:63.286; most accessible tissue: Minghui63 panicle, score: 75.788	N	N	N	N
vg0118939890	A -> G	LOC_Os01g34330-LOC_Os01g34350	intergenic_region ; MODIFIER	silent_mutation	Average:63.286; most accessible tissue: Minghui63 panicle, score: 75.788	N	N	N	N
vg0118939890	A -> DEL	N	N	silent_mutation	Average:63.286; most accessible tissue: Minghui63 panicle, score: 75.788	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0118939890	6.90E-07	6.90E-07	mr1621	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
vg0118939890	NA	6.14E-15	mr1902_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