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Detailed information for vg0401887481:

Variant ID: vg0401887481 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 1887481
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 281. )

Flanking Sequence (100 bp) in Reference Genome:

GAACTTGGGAAACCAATATGGATACAATCCGAATAGTCCTTGTCGTTTCCGTGTAGAACTCTGGTTGCCTTTCCTTATTGGAACTCCTCCTATATCCGAA[G/T]
GTTGCTTCCGTATAGGACATGGTATGTGGTGAGCCCTGTCGAGATTTAGTCAACTACTATTAGGTATGTGGTATCCATAACCCTGACAGTAGCCCCCGAC

Reverse complement sequence

GTCGGGGGCTACTGTCAGGGTTATGGATACCACATACCTAATAGTAGTTGACTAAATCTCGACAGGGCTCACCACATACCATGTCCTATACGGAAGCAAC[C/A]
TTCGGATATAGGAGGAGTTCCAATAAGGAAAGGCAACCAGAGTTCTACACGGAAACGACAAGGACTATTCGGATTGTATCCATATTGGTTTCCCAAGTTC

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	93.80%	0.30%	0.97%	5.01%	NA
All Indica	2759	99.50%	0.00%	0.14%	0.33%	NA
All Japonica	1512	81.70%	0.80%	2.71%	14.81%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.60%	0.00%	0.00%	0.43%	NA
Indica III	913	99.80%	0.00%	0.11%	0.11%	NA
Indica Intermediate	786	98.90%	0.00%	0.38%	0.76%	NA
Temperate Japonica	767	90.00%	0.00%	0.39%	9.65%	NA
Tropical Japonica	504	70.00%	1.80%	6.15%	22.02%	NA
Japonica Intermediate	241	79.70%	1.20%	2.90%	16.18%	NA
VI/Aromatic	96	95.80%	0.00%	1.04%	3.12%	NA
Intermediate	90	98.90%	0.00%	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
vg0401887481	G -> DEL	N	N	silent_mutation	Average:53.432; most accessible tissue: Minghui63 young leaf, score: 77.243	N	N	N	N
vg0401887481	G -> T	LOC_Os04g04080.1	downstream_gene_variant ; 2763.0bp to feature; MODIFIER	silent_mutation	Average:53.432; most accessible tissue: Minghui63 young leaf, score: 77.243	N	N	N	N
vg0401887481	G -> T	LOC_Os04g04080-LOC_Os04g04100	intergenic_region ; MODIFIER	silent_mutation	Average:53.432; most accessible tissue: Minghui63 young leaf, score: 77.243	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0401887481	NA	2.48E-06	mr1040	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
vg0401887481	NA	6.07E-06	mr1155	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
vg0401887481	NA	1.09E-07	mr1194	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
vg0401887481	NA	1.48E-07	mr1213	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
vg0401887481	NA	2.21E-06	mr1225	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
vg0401887481	NA	6.05E-16	mr1301	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
vg0401887481	4.26E-06	2.37E-16	mr1410	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
vg0401887481	NA	1.40E-06	mr1805	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
vg0401887481	1.78E-08	2.64E-20	mr1301_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
vg0401887481	1.32E-07	7.05E-18	mr1410_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
vg0401887481	NA	1.74E-08	mr1676_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
vg0401887481	6.05E-06	NA	mr1798_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