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Detailed information for vg1103575882:

Variant ID: vg1103575882 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 3575882
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 77. )

Flanking Sequence (100 bp) in Reference Genome:

TTAATTAATTACGTGCTAATGGATCGCTCCGTTTTTCGCGTGGAGGAGACGTGGGTTCCCAACCCGAAGGAGCTAACAGAGTGTTAGCTTGCTTTTCATC[G/A]
CATGTGCCATTATGGAGCATAGTACTTCCAAGCTAGTGTAAGACTCTGCATCTAATTAGGTTTCAAAAATAAAAGACTCTGCATCTAAAACCTGCATTAA

Reverse complement sequence

TTAATGCAGGTTTTAGATGCAGAGTCTTTTATTTTTGAAACCTAATTAGATGCAGAGTCTTACACTAGCTTGGAAGTACTATGCTCCATAATGGCACATG[C/T]
GATGAAAAGCAAGCTAACACTCTGTTAGCTCCTTCGGGTTGGGAACCCACGTCTCCTCCACGCGAAAAACGGAGCGATCCATTAGCACGTAATTAATTAA

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	49.50%	47.80%	0.08%	2.62%	NA
All Indica	2759	69.70%	28.20%	0.11%	2.03%	NA
All Japonica	1512	8.90%	91.10%	0.00%	0.00%	NA
Aus	269	71.40%	3.30%	0.37%	24.91%	NA
Indica I	595	95.00%	1.20%	0.17%	3.70%	NA
Indica II	465	33.80%	65.80%	0.22%	0.22%	NA
Indica III	913	75.50%	22.80%	0.00%	1.75%	NA
Indica Intermediate	786	65.10%	32.60%	0.13%	2.16%	NA
Temperate Japonica	767	1.20%	98.80%	0.00%	0.00%	NA
Tropical Japonica	504	21.20%	78.80%	0.00%	0.00%	NA
Japonica Intermediate	241	7.50%	92.50%	0.00%	0.00%	NA
VI/Aromatic	96	53.10%	46.90%	0.00%	0.00%	NA
Intermediate	90	44.40%	54.40%	0.00%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1103575882	G -> A	LOC_Os11g07160-LOC_Os11g07170	intergenic_region ; MODIFIER	silent_mutation	Average:45.503; most accessible tissue: Minghui63 young leaf, score: 65.161	N	N	N	N
vg1103575882	G -> DEL	N	N	silent_mutation	Average:45.503; most accessible tissue: Minghui63 young leaf, score: 65.161	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1103575882	NA	1.21E-06	mr1231	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
vg1103575882	NA	2.15E-06	mr1232	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
vg1103575882	NA	3.93E-09	mr1399	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
vg1103575882	1.85E-06	4.76E-15	mr1557	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
vg1103575882	3.74E-06	2.32E-12	mr1598	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
vg1103575882	NA	3.62E-08	mr1662	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
vg1103575882	NA	2.59E-09	mr1944	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
vg1103575882	NA	6.48E-06	mr1265_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
vg1103575882	NA	1.07E-07	mr1360_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
vg1103575882	NA	9.71E-06	mr1497_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
vg1103575882	NA	1.20E-06	mr1531_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
vg1103575882	NA	4.83E-10	mr1557_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
vg1103575882	NA	2.46E-07	mr1593_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
vg1103575882	NA	2.63E-11	mr1598_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
vg1103575882	NA	2.00E-09	mr1829_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
vg1103575882	NA	7.28E-07	mr1842_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
vg1103575882	NA	1.14E-06	mr1895_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
vg1103575882	NA	3.64E-10	mr1902_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
vg1103575882	NA	7.78E-13	mr1904_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
vg1103575882	NA	6.64E-07	mr1933_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