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Detailed information for vg0407576542:

Variant ID: vg0407576542 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 7576542
Reference Allele: A	Alternative Allele: T
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.66, T: 0.34, others allele: 0.00, population size: 89. )

Flanking Sequence (100 bp) in Reference Genome:

CAGATAGCGTCCGTTACAGATGACTACTAACCTCAATCGGGTACTAAGTTATGACCCGTCACAAATGAGTATAATCCACAAAAAATATTAATTTTGTTTT[A/T]
TGGCTAGCTTCAGGCCTTTGCTAGCCATACCCGCTGTAAAAATGACAGAAACACATGCATATACAATATCCCCAGCATCACCCATTCATATACATGCATT

Reverse complement sequence

AATGCATGTATATGAATGGGTGATGCTGGGGATATTGTATATGCATGTGTTTCTGTCATTTTTACAGCGGGTATGGCTAGCAAAGGCCTGAAGCTAGCCA[T/A]
AAAACAAAATTAATATTTTTTGTGGATTATACTCATTTGTGACGGGTCATAACTTAGTACCCGATTGAGGTTAGTAGTCATCTGTAACGGACGCTATCTG

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	22.00%	13.80%	0.32%	63.86%	NA
All Indica	2759	1.80%	2.00%	0.43%	95.69%	NA
All Japonica	1512	63.30%	35.20%	0.00%	1.52%	NA
Aus	269	0.40%	0.00%	0.37%	99.26%	NA
Indica I	595	2.20%	0.20%	0.17%	97.48%	NA
Indica II	465	2.20%	2.60%	0.86%	94.41%	NA
Indica III	913	1.00%	3.00%	0.55%	95.51%	NA
Indica Intermediate	786	2.40%	2.00%	0.25%	95.29%	NA
Temperate Japonica	767	96.00%	3.50%	0.00%	0.52%	NA
Tropical Japonica	504	9.90%	87.30%	0.00%	2.78%	NA
Japonica Intermediate	241	71.00%	27.00%	0.00%	2.07%	NA
VI/Aromatic	96	8.30%	42.70%	1.04%	47.92%	NA
Intermediate	90	25.60%	26.70%	1.11%	46.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0407576542	A -> DEL	N	N	silent_mutation	Average:10.421; most accessible tissue: Callus, score: 54.711	N	N	N	N
vg0407576542	A -> T	LOC_Os04g13560.1	downstream_gene_variant ; 741.0bp to feature; MODIFIER	silent_mutation	Average:10.421; most accessible tissue: Callus, score: 54.711	N	N	N	N
vg0407576542	A -> T	LOC_Os04g13550-LOC_Os04g13560	intergenic_region ; MODIFIER	silent_mutation	Average:10.421; most accessible tissue: Callus, score: 54.711	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0407576542	1.49E-08	NA	mr1071	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
vg0407576542	3.21E-06	NA	mr1080	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
vg0407576542	7.19E-08	NA	mr1140	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
vg0407576542	1.55E-07	NA	mr1203	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
vg0407576542	7.57E-06	2.78E-23	mr1301	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
vg0407576542	NA	3.12E-15	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
vg0407576542	5.61E-07	NA	mr1618	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
vg0407576542	NA	9.94E-09	mr1648	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
vg0407576542	NA	8.28E-07	mr1993	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
vg0407576542	NA	6.08E-08	mr1993	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
vg0407576542	1.72E-07	NA	mr1071_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
vg0407576542	3.06E-09	NA	mr1080_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
vg0407576542	3.79E-06	NA	mr1100_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
vg0407576542	9.55E-10	NA	mr1203_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
vg0407576542	NA	1.00E-22	mr1301_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
vg0407576542	NA	2.04E-18	mr1301_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
vg0407576542	NA	5.41E-06	mr1398_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
vg0407576542	8.01E-08	NA	mr1613_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
vg0407576542	1.20E-07	NA	mr1619_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
vg0407576542	NA	2.21E-11	mr1993_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
vg0407576542	NA	1.57E-12	mr1993_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