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Detailed information for vg0717334017:

Variant ID: vg0717334017 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 17334017
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.97, C: 0.03, others allele: 0.00, population size: 232. )

Flanking Sequence (100 bp) in Reference Genome:

GATGGGACTAAATATACACAAATCAGGGTCCACTCTAGTTAGTGGATTCTCTGATGCAGACTGGGCTGGTAGCATAGATGACAGAAGGTCAACTAGTGGA[T/C]
TTGCTATCTTTATTGGTTCTAATCTAGTGTCATGGAATGCTAGAAAACAGGCCACAGTATCAAGATCTATTACAGAGTCAGAATACAAAGCAATAGCCAA

Reverse complement sequence

TTGGCTATTGCTTTGTATTCTGACTCTGTAATAGATCTTGATACTGTGGCCTGTTTTCTAGCATTCCATGACACTAGATTAGAACCAATAAAGATAGCAA[A/G]
TCCACTAGTTGACCTTCTGTCATCTATGCTACCAGCCCAGTCTGCATCAGAGAATCCACTAACTAGAGTGGACCCTGATTTGTGTATATTTAGTCCCATC

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	61.80%	38.20%	0.04%	0.00%	NA
All Indica	2759	36.60%	63.40%	0.04%	0.00%	NA
All Japonica	1512	99.30%	0.70%	0.00%	0.00%	NA
Aus	269	91.80%	7.80%	0.37%	0.00%	NA
Indica I	595	43.70%	56.30%	0.00%	0.00%	NA
Indica II	465	16.30%	83.70%	0.00%	0.00%	NA
Indica III	913	40.10%	59.90%	0.00%	0.00%	NA
Indica Intermediate	786	39.10%	60.80%	0.13%	0.00%	NA
Temperate Japonica	767	99.10%	0.90%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.80%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	74.40%	25.60%	0.00%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0717334017	T -> C	LOC_Os07g29520.1	missense_variant ; p.Phe814Leu; MODERATE	nonsynonymous_codon ; F814L	Average:41.489; most accessible tissue: Zhenshan97 young leaf, score: 49.329	benign	1.429	DELETERIOUS	0.00

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0717334017	4.14E-06	1.20E-06	mr1086	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
vg0717334017	NA	5.09E-06	mr1104	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
vg0717334017	1.88E-07	5.02E-08	mr1107	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
vg0717334017	NA	2.34E-06	mr1139	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
vg0717334017	3.52E-06	2.38E-06	mr1241	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
vg0717334017	2.01E-06	NA	mr1246	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
vg0717334017	7.78E-06	5.17E-07	mr1246	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
vg0717334017	9.29E-06	NA	mr1404	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
vg0717334017	NA	1.99E-06	mr1437	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
vg0717334017	NA	1.38E-07	mr1559	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
vg0717334017	NA	4.40E-07	mr1676	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
vg0717334017	2.84E-06	NA	mr1878	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
vg0717334017	3.02E-06	2.77E-06	mr1878	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
vg0717334017	3.60E-06	NA	mr1949	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
vg0717334017	NA	4.10E-07	mr1973	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
vg0717334017	NA	8.33E-08	mr1246_2	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