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Detailed information for vg0408410720:

Variant ID: vg0408410720 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 8410720
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 232. )

Flanking Sequence (100 bp) in Reference Genome:

CTACCTTGTGTTCAACCAAATTTCAAATAATCTCATTTCTCAAAACATATTCTTGGAAAAGAACACATGTGGGTAATCATCGTGAGATGTAGACCTCTGT[G/A]
AGATGGGCGAGGTGCTCGCTGCCTATGTTATGACCAGTGCGGCCAATTTCTAGGGCTCTATCGGGTAATCATCTCAAAATGTAGACCACTTTATGATGGG

Reverse complement sequence

CCCATCATAAAGTGGTCTACATTTTGAGATGATTACCCGATAGAGCCCTAGAAATTGGCCGCACTGGTCATAACATAGGCAGCGAGCACCTCGCCCATCT[C/T]
ACAGAGGTCTACATCTCACGATGATTACCCACATGTGTTCTTTTCCAAGAATATGTTTTGAGAAATGAGATTATTTGAAATTTGGTTGAACACAAGGTAG

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	37.90%	5.10%	16.74%	40.25%	NA
All Indica	2759	25.40%	0.30%	23.38%	51.00%	NA
All Japonica	1512	63.00%	14.50%	4.03%	18.45%	NA
Aus	269	13.40%	0.00%	18.22%	68.40%	NA
Indica I	595	8.20%	0.00%	8.91%	82.86%	NA
Indica II	465	19.40%	1.10%	23.66%	55.91%	NA
Indica III	913	38.00%	0.00%	39.21%	22.78%	NA
Indica Intermediate	786	27.20%	0.30%	15.78%	56.74%	NA
Temperate Japonica	767	96.30%	0.00%	0.52%	3.13%	NA
Tropical Japonica	504	8.50%	40.90%	10.52%	40.08%	NA
Japonica Intermediate	241	71.00%	5.40%	1.66%	21.99%	NA
VI/Aromatic	96	69.80%	8.30%	16.67%	5.21%	NA
Intermediate	90	37.80%	10.00%	22.22%	30.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0408410720	G -> DEL	N	N	silent_mutation	Average:12.509; most accessible tissue: Callus, score: 34.144	N	N	N	N
vg0408410720	G -> A	LOC_Os04g14960.1	upstream_gene_variant ; 1758.0bp to feature; MODIFIER	silent_mutation	Average:12.509; most accessible tissue: Callus, score: 34.144	N	N	N	N
vg0408410720	G -> A	LOC_Os04g14970.1	intron_variant ; MODIFIER	silent_mutation	Average:12.509; most accessible tissue: Callus, score: 34.144	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0408410720	NA	3.03E-07	mr1423	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
vg0408410720	NA	7.07E-07	mr1599	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
vg0408410720	7.35E-06	NA	mr1022_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
vg0408410720	NA	2.85E-13	mr1022_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
vg0408410720	2.03E-07	NA	mr1023_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
vg0408410720	NA	1.08E-09	mr1023_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
vg0408410720	5.90E-07	NA	mr1055_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
vg0408410720	NA	3.48E-13	mr1055_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
vg0408410720	3.22E-07	NA	mr1079_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
vg0408410720	NA	3.14E-12	mr1079_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
vg0408410720	NA	3.18E-10	mr1093_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
vg0408410720	6.31E-08	NA	mr1132_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
vg0408410720	NA	9.45E-12	mr1132_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
vg0408410720	NA	3.31E-06	mr1243_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
vg0408410720	NA	1.89E-06	mr1248_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
vg0408410720	NA	4.13E-07	mr1257_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
vg0408410720	2.35E-07	NA	mr1390_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
vg0408410720	NA	1.81E-13	mr1390_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
vg0408410720	NA	8.93E-07	mr1423_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
vg0408410720	8.96E-09	NA	mr1489_2	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
vg0408410720	NA	6.62E-08	mr1489_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
vg0408410720	5.02E-07	NA	mr1490_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
vg0408410720	NA	4.37E-13	mr1490_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
vg0408410720	4.77E-07	NA	mr1778_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