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Detailed information for vg0403239751:

Variant ID: vg0403239751 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 3239751
Reference Allele: C	Alternative Allele: T,A
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, T: 0.01, others allele: 0.00, population size: 86. )

Flanking Sequence (100 bp) in Reference Genome:

GGTCGTTCAACTCCACTCTTGCGTCTCCACATCCCGTAACCAAAGGTAAGCAACAGCGACTCTCTCCATACCAAAATATAAGAAGTTTTAGAATTGGACA[C/T,A]
GGTTACTAAGAATAGGCGTAGAATTAAACGGGAAGATGTTGTGATTGGTTGAGAAGTGGAGGTAAGTGAGAAAAATGAATGTTGGAGGGTTCTGATTGGT

Reverse complement sequence

ACCAATCAGAACCCTCCAACATTCATTTTTCTCACTTACCTCCACTTCTCAACCAATCACAACATCTTCCCGTTTAATTCTACGCCTATTCTTAGTAACC[G/A,T]
TGTCCAATTCTAAAACTTCTTATATTTTGGTATGGAGAGAGTCGCTGTTGCTTACCTTTGGTTACGGGATGTGGAGACGCAAGAGTGGAGTTGAACGACC

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	72.40%	14.20%	1.38%	11.98%	NA
All Indica	2759	80.00%	9.30%	0.51%	10.18%	NA
All Japonica	1512	63.00%	25.60%	2.71%	8.73%	NA
Aus	269	39.80%	4.80%	2.97%	52.42%	NA
Indica I	595	94.50%	5.20%	0.17%	0.17%	NA
Indica II	465	98.30%	1.10%	0.22%	0.43%	NA
Indica III	913	62.80%	11.20%	0.55%	25.52%	NA
Indica Intermediate	786	78.20%	15.10%	0.89%	5.73%	NA
Temperate Japonica	767	79.10%	5.60%	3.65%	11.60%	NA
Tropical Japonica	504	34.10%	56.30%	2.58%	6.94%	NA
Japonica Intermediate	241	71.80%	24.90%	0.00%	3.32%	NA
VI/Aromatic	96	88.50%	8.30%	0.00%	3.12%	NA
Intermediate	90	78.90%	8.90%	2.22%	10.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0403239751	C -> DEL	N	N	silent_mutation	Average:23.774; most accessible tissue: Zhenshan97 panicle, score: 39.652	N	N	N	N
vg0403239751	C -> A	LOC_Os04g06230.1	upstream_gene_variant ; 4316.0bp to feature; MODIFIER	N	Average:23.774; most accessible tissue: Zhenshan97 panicle, score: 39.652	N	N	N	N
vg0403239751	C -> A	LOC_Os04g06244.1	intron_variant ; MODIFIER	N	Average:23.774; most accessible tissue: Zhenshan97 panicle, score: 39.652	N	N	N	N
vg0403239751	C -> T	LOC_Os04g06230.1	upstream_gene_variant ; 4316.0bp to feature; MODIFIER	silent_mutation	Average:23.774; most accessible tissue: Zhenshan97 panicle, score: 39.652	N	N	N	N
vg0403239751	C -> T	LOC_Os04g06244.1	intron_variant ; MODIFIER	silent_mutation	Average:23.774; most accessible tissue: Zhenshan97 panicle, score: 39.652	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0403239751	NA	7.10E-06	mr1100	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
vg0403239751	NA	1.99E-09	mr1458	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
vg0403239751	NA	1.18E-09	mr1563	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
vg0403239751	NA	1.17E-06	mr1668	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
vg0403239751	NA	8.52E-08	mr1757	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
vg0403239751	NA	1.08E-09	mr1980	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
vg0403239751	NA	6.26E-11	mr1563_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