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Detailed information for vg0105889711:

Variant ID: vg0105889711 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 5889711
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.02, others allele: 0.00, population size: 109. )

Flanking Sequence (100 bp) in Reference Genome:

CATTCTCCTCGACTGCGTGTTCGCTCGGCAGGTCTGGCTCCGGGTGTTGTCGCCTTCTGGCCGGTCTGCCCTCTCTCCACCCCGTGGCAATTGGTTCCAG[G/A]
ACTGGTGGCCATCCTCTAGGGCCTGCTTACCAGAGCACCTCCGCGACAGCTTCGACTCCATGGTGCTCCTGGTCTCTTGGTGTCTGTGGAAGGAGCGGAA

Reverse complement sequence

TTCCGCTCCTTCCACAGACACCAAGAGACCAGGAGCACCATGGAGTCGAAGCTGTCGCGGAGGTGCTCTGGTAAGCAGGCCCTAGAGGATGGCCACCAGT[C/T]
CTGGAACCAATTGCCACGGGGTGGAGAGAGGGCAGACCGGCCAGAAGGCGACAACACCCGGAGCCAGACCTGCCGAGCGAACACGCAGTCGAGGAGAATG

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	78.30%	21.70%	0.00%	0.00%	NA
All Indica	2759	84.10%	15.90%	0.00%	0.00%	NA
All Japonica	1512	79.40%	20.60%	0.00%	0.00%	NA
Aus	269	10.80%	89.20%	0.00%	0.00%	NA
Indica I	595	91.60%	8.40%	0.00%	0.00%	NA
Indica II	465	78.50%	21.50%	0.00%	0.00%	NA
Indica III	913	92.70%	7.30%	0.00%	0.00%	NA
Indica Intermediate	786	71.60%	28.40%	0.00%	0.00%	NA
Temperate Japonica	767	95.70%	4.30%	0.00%	0.00%	NA
Tropical Japonica	504	70.20%	29.80%	0.00%	0.00%	NA
Japonica Intermediate	241	46.90%	53.10%	0.00%	0.00%	NA
VI/Aromatic	96	83.30%	16.70%	0.00%	0.00%	NA
Intermediate	90	81.10%	18.90%	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
vg0105889711	G -> A	LOC_Os01g11040.1	upstream_gene_variant ; 894.0bp to feature; MODIFIER	silent_mutation	Average:59.768; most accessible tissue: Minghui63 flower, score: 70.218	N	N	N	N
vg0105889711	G -> A	LOC_Os01g11020-LOC_Os01g11040	intergenic_region ; MODIFIER	silent_mutation	Average:59.768; most accessible tissue: Minghui63 flower, score: 70.218	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0105889711	NA	3.03E-06	mr1180	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
vg0105889711	4.01E-06	NA	mr1498	Ind_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
vg0105889711	9.39E-08	1.20E-11	mr1769	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
vg0105889711	NA	6.26E-06	mr1943	Ind_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
vg0105889711	5.18E-06	NA	mr1951	Ind_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
vg0105889711	NA	3.35E-06	mr1155_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
vg0105889711	NA	2.30E-08	mr1180_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
vg0105889711	NA	7.43E-08	mr1183_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
vg0105889711	NA	1.27E-10	mr1310_2	Ind_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
vg0105889711	NA	1.33E-07	mr1498_2	Ind_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
vg0105889711	NA	1.97E-07	mr1740_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
vg0105889711	9.12E-06	6.75E-12	mr1769_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
vg0105889711	NA	6.28E-12	mr1769_2	Ind_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
vg0105889711	NA	1.66E-07	mr1794_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
vg0105889711	NA	5.71E-09	mr1829_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
vg0105889711	NA	1.85E-06	mr1924_2	Ind_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
vg0105889711	NA	9.05E-09	mr1943_2	Ind_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