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Detailed information for vg0409081774:

Variant ID: vg0409081774 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 9081774
Reference Allele: G	Alternative Allele: C
Primary Allele: G	Secondary Allele: C

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 313. )

Flanking Sequence (100 bp) in Reference Genome:

TAATGCCCACTTTAGAGGTCTAAGATCCTCCCCTGCGACTACATTAATTGTAGGTGCCCTAAGATTCACATACCAGAGGGGCTTCCCATACTTTTTTTAA[G/C]
GTAAAACAAAGGCCAGTGTATTGAAAACTGGGATGGTTGAAGAAGCTGTAGATGAACTTGCGGCTATTTAGGTGAAGATATATGGCATCCCGAAATTGGC

Reverse complement sequence

GCCAATTTCGGGATGCCATATATCTTCACCTAAATAGCCGCAAGTTCATCTACAGCTTCTTCAACCATCCCAGTTTTCAATACACTGGCCTTTGTTTTAC[C/G]
TTAAAAAAAGTATGGGAAGCCCCTCTGGTATGTGAATCTTAGGGCACCTACAATTAATGTAGTCGCAGGGGAGGATCTTAGACCTCTAAAGTGGGCATTA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	85.30%	14.40%	0.23%	0.08%	NA
All Indica	2759	99.50%	0.40%	0.04%	0.00%	NA
All Japonica	1512	62.00%	37.60%	0.33%	0.07%	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	98.70%	1.10%	0.22%	0.00%	NA
Indica III	913	99.80%	0.20%	0.00%	0.00%	NA
Indica Intermediate	786	99.40%	0.60%	0.00%	0.00%	NA
Temperate Japonica	767	96.30%	3.70%	0.00%	0.00%	NA
Tropical Japonica	504	5.60%	93.50%	0.79%	0.20%	NA
Japonica Intermediate	241	70.50%	29.00%	0.41%	0.00%	NA
VI/Aromatic	96	14.60%	82.30%	2.08%	1.04%	NA
Intermediate	90	72.20%	22.20%	3.33%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0409081774	G -> C	LOC_Os04g16680.1	upstream_gene_variant ; 3886.0bp to feature; MODIFIER	silent_mutation	Average:57.072; most accessible tissue: Minghui63 flag leaf, score: 80.516	N	N	N	N
vg0409081774	G -> C	LOC_Os04g16700.1	downstream_gene_variant ; 3290.0bp to feature; MODIFIER	silent_mutation	Average:57.072; most accessible tissue: Minghui63 flag leaf, score: 80.516	N	N	N	N
vg0409081774	G -> C	LOC_Os04g16690.1	intron_variant ; MODIFIER	silent_mutation	Average:57.072; most accessible tissue: Minghui63 flag leaf, score: 80.516	N	N	N	N
vg0409081774	G -> DEL	N	N	silent_mutation	Average:57.072; most accessible tissue: Minghui63 flag leaf, score: 80.516	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0409081774	NA	3.82E-06	mr1045	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
vg0409081774	NA	2.17E-06	mr1090	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
vg0409081774	NA	9.29E-08	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
vg0409081774	NA	1.11E-06	mr1206	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
vg0409081774	NA	1.64E-13	mr1330	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
vg0409081774	NA	5.73E-07	mr1403	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
vg0409081774	NA	4.87E-14	mr1454	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
vg0409081774	NA	3.88E-11	mr1454	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
vg0409081774	NA	2.90E-07	mr1642	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
vg0409081774	NA	3.67E-07	mr1715	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
vg0409081774	NA	3.57E-07	mr1739	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
vg0409081774	NA	3.46E-13	mr1789	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
vg0409081774	NA	4.95E-12	mr1864	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
vg0409081774	NA	2.12E-09	mr1880	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
vg0409081774	NA	1.21E-09	mr1398_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
vg0409081774	NA	8.97E-14	mr1454_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