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Detailed information for vg0403207821:

Variant ID: vg0403207821 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 3207821
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.82, G: 0.21, others allele: 0.00, population size: 28. )

Flanking Sequence (100 bp) in Reference Genome:

TCGCCTTGTGCAGGTCCGAGTGCATCCTATCCAATCCCCTCATCACAGCACACATGTGACCAAAGGTAGTGTCGTTCTCGCCGGCTGTTGGACGGAAGGT[G/A]
CTGACATCATCACCGTTGGCTCGACGAGGGTGGAAGCGGTACGCCGTGTCATGGAAGATGTAGTTGTGGCGCTCCCGTAGTCTGGCCATCATCAGGTATG

Reverse complement sequence

CATACCTGATGATGGCCAGACTACGGGAGCGCCACAACTACATCTTCCATGACACGGCGTACCGCTTCCACCCTCGTCGAGCCAACGGTGATGATGTCAG[C/T]
ACCTTCCGTCCAACAGCCGGCGAGAACGACACTACCTTTGGTCACATGTGTGCTGTGATGAGGGGATTGGATAGGATGCACTCGGACCTGCACAAGGCGA

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	44.10%	5.40%	34.55%	16.00%	NA
All Indica	2759	13.60%	8.50%	52.52%	25.34%	NA
All Japonica	1512	91.40%	0.50%	5.42%	2.65%	NA
Aus	269	72.10%	1.10%	26.39%	0.37%	NA
Indica I	595	8.60%	4.70%	37.98%	48.74%	NA
Indica II	465	15.50%	0.60%	45.81%	38.06%	NA
Indica III	913	10.30%	18.20%	65.06%	6.46%	NA
Indica Intermediate	786	20.20%	4.80%	52.93%	22.01%	NA
Temperate Japonica	767	93.60%	0.00%	4.04%	2.35%	NA
Tropical Japonica	504	89.90%	1.40%	6.15%	2.58%	NA
Japonica Intermediate	241	87.60%	0.40%	8.30%	3.73%	NA
VI/Aromatic	96	91.70%	0.00%	8.33%	0.00%	NA
Intermediate	90	47.80%	8.90%	25.56%	17.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0403207821	G -> DEL	LOC_Os04g06160.1	N	frameshift_variant	Average:18.41; most accessible tissue: Zhenshan97 root, score: 38.035	N	N	N	N
vg0403207821	G -> A	LOC_Os04g06160.1	synonymous_variant ; p.Ser114Ser; LOW	synonymous_codon	Average:18.41; most accessible tissue: Zhenshan97 root, score: 38.035	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0403207821	2.87E-06	6.87E-08	mr1117	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
vg0403207821	NA	9.35E-06	mr1119	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
vg0403207821	NA	8.28E-06	mr1247	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
vg0403207821	NA	1.89E-07	mr1496	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
vg0403207821	NA	7.20E-06	mr1113_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
vg0403207821	1.66E-07	7.14E-09	mr1117_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
vg0403207821	7.73E-06	2.56E-06	mr1118_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
vg0403207821	8.86E-07	1.40E-07	mr1119_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
vg0403207821	4.54E-06	2.54E-06	mr1120_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
vg0403207821	2.25E-06	8.03E-06	mr1123_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
vg0403207821	5.14E-06	4.05E-07	mr1240_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
vg0403207821	3.64E-06	2.67E-06	mr1247_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
vg0403207821	2.62E-08	8.21E-10	mr1496_2	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
vg0403207821	3.57E-08	1.96E-08	mr1961_2	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