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Detailed information for vg0627787332:

Variant ID: vg0627787332 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 27787332
Reference Allele: G	Alternative Allele: T
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 309. )

Flanking Sequence (100 bp) in Reference Genome:

GCCCAGTTTGTTCATCGAATACTTGCCTGAGCTATATCACTAGATTTCGTAGGCATTCATCATCCAGTTATTCAGTTGTGTTGTACATCAGCCTCTTAGA[G/T]
CTGTTATCCTAACAGGGCTCCAACTGAATTACCTATGCAATAACTGTTGGTGTTTATTGAAAGGCATATACTTTAGTTGCAGCATGTAAACACACCTTTT

Reverse complement sequence

AAAAGGTGTGTTTACATGCTGCAACTAAAGTATATGCCTTTCAATAAACACCAACAGTTATTGCATAGGTAATTCAGTTGGAGCCCTGTTAGGATAACAG[C/A]
TCTAAGAGGCTGATGTACAACACAACTGAATAACTGGATGATGAATGCCTACGAAATCTAGTGATATAGCTCAGGCAAGTATTCGATGAACAAACTGGGC

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	83.20%	11.70%	5.12%	0.00%	NA
All Indica	2759	94.90%	0.40%	4.78%	0.00%	NA
All Japonica	1512	58.10%	35.40%	6.55%	0.00%	NA
Aus	269	98.50%	0.40%	1.12%	0.00%	NA
Indica I	595	87.40%	1.20%	11.43%	0.00%	NA
Indica II	465	93.50%	0.20%	6.24%	0.00%	NA
Indica III	913	99.70%	0.10%	0.22%	0.00%	NA
Indica Intermediate	786	95.70%	0.10%	4.20%	0.00%	NA
Temperate Japonica	767	36.00%	55.90%	8.08%	0.00%	NA
Tropical Japonica	504	88.50%	6.70%	4.76%	0.00%	NA
Japonica Intermediate	241	64.70%	29.90%	5.39%	0.00%	NA
VI/Aromatic	96	99.00%	0.00%	1.04%	0.00%	NA
Intermediate	90	85.60%	6.70%	7.78%	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
vg0627787332	G -> T	LOC_Os06g45900.1	intron_variant ; MODIFIER	silent_mutation	Average:45.496; most accessible tissue: Zhenshan97 young leaf, score: 65.804	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0627787332	NA	1.02E-14	Spikelet_length	All	Not	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0627787332	7.08E-06	NA	mr1554	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
vg0627787332	NA	3.23E-06	mr1554	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
vg0627787332	3.82E-06	3.82E-06	mr1952	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
vg0627787332	NA	1.14E-07	mr1010_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
vg0627787332	NA	2.09E-06	mr1554_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