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Detailed information for vg1109530380:

Variant ID: vg1109530380 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 9530380
Reference Allele: T	Alternative Allele: G
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: 66. )

Flanking Sequence (100 bp) in Reference Genome:

TCAATACCTCCTATCTCCCTCTGCATGGTCCCGCGGCCAGGGAGGGTGCCGTCGTCCTGCAACTTCTTCAGGGATGCGGTGGTGGAGGTGGACTTGTCGA[T/G]
ATCCATCGCCGCCGGAGGATCGCCGGAGAGTAAAGCGAAAGAGGCAAGCTAGGGTTTTCCCTACGGGAGCGGAGATGACGAAGGGCGCTTGAAGACTTGA

Reverse complement sequence

TCAAGTCTTCAAGCGCCCTTCGTCATCTCCGCTCCCGTAGGGAAAACCCTAGCTTGCCTCTTTCGCTTTACTCTCCGGCGATCCTCCGGCGGCGATGGAT[A/C]
TCGACAAGTCCACCTCCACCACCGCATCCCTGAAGAAGTTGCAGGACGACGGCACCCTCCCTGGCCGCGGGACCATGCAGAGGGAGATAGGAGGTATTGA

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	35.00%	14.50%	3.72%	46.76%	NA
All Indica	2759	4.90%	24.70%	6.02%	64.41%	NA
All Japonica	1512	96.00%	0.10%	0.13%	3.84%	NA
Aus	269	4.50%	0.00%	2.60%	92.94%	NA
Indica I	595	8.90%	15.60%	3.53%	71.93%	NA
Indica II	465	3.40%	17.40%	4.30%	74.84%	NA
Indica III	913	1.80%	38.70%	8.98%	50.60%	NA
Indica Intermediate	786	6.20%	19.70%	5.47%	68.58%	NA
Temperate Japonica	767	97.10%	0.10%	0.00%	2.74%	NA
Tropical Japonica	504	94.60%	0.00%	0.40%	4.96%	NA
Japonica Intermediate	241	95.00%	0.00%	0.00%	4.98%	NA
VI/Aromatic	96	18.80%	0.00%	0.00%	81.25%	NA
Intermediate	90	44.40%	2.20%	1.11%	52.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1109530380	T -> DEL	LOC_Os11g17160.1	N	frameshift_variant	Average:18.018; most accessible tissue: Minghui63 root, score: 35.002	N	N	N	N
vg1109530380	T -> G	LOC_Os11g17160.1	missense_variant ; p.Ile3Leu; MODERATE	nonsynonymous_codon ; I3L	Average:18.018; most accessible tissue: Minghui63 root, score: 35.002	unknown	unknown	TOLERATED	1.00

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1109530380	NA	2.74E-09	mr1986	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
vg1109530380	1.96E-06	1.96E-06	mr1025_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
vg1109530380	NA	2.78E-06	mr1027_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
vg1109530380	3.18E-06	6.97E-06	mr1306_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
vg1109530380	NA	1.53E-07	mr1376_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
vg1109530380	3.64E-06	NA	mr1376_2	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
vg1109530380	6.68E-06	1.25E-06	mr1409_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
vg1109530380	NA	9.06E-08	mr1431_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
vg1109530380	5.08E-06	5.08E-06	mr1463_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
vg1109530380	3.25E-06	5.42E-06	mr1505_2	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
vg1109530380	NA	5.36E-06	mr1649_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
vg1109530380	4.91E-06	4.91E-06	mr1736_2	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
vg1109530380	NA	8.56E-09	mr1835_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
vg1109530380	2.46E-06	1.98E-06	mr1849_2	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