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Detailed information for vg0706750728:

Variant ID: vg0706750728 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 6750728
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.74, T: 0.26, others allele: 0.00, population size: 82. )

Flanking Sequence (100 bp) in Reference Genome:

ACTGCATGTGGAGGATATATGGGTTAATGTATCACATGCTAAATATATTTGTTACTACACAAAAGTGGAGTGTTATTGCAAAGGCAGGTACACGTTACCA[C/T]
ATATTTATGCAGTAACACTATCCAAAAAATACAGTAAAACACAGTTACTGCAAAAACTTATAATTTTTGCTGCACTCTTACAGTAATGATGCGATGGGAT

Reverse complement sequence

ATCCCATCGCATCATTACTGTAAGAGTGCAGCAAAAATTATAAGTTTTTGCAGTAACTGTGTTTTACTGTATTTTTTGGATAGTGTTACTGCATAAATAT[G/A]
TGGTAACGTGTACCTGCCTTTGCAATAACACTCCACTTTTGTGTAGTAACAAATATATTTAGCATGTGATACATTAACCCATATATCCTCCACATGCAGT

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	60.60%	37.70%	0.76%	0.91%	NA
All Indica	2759	93.80%	3.70%	1.12%	1.41%	NA
All Japonica	1512	0.50%	99.50%	0.07%	0.00%	NA
Aus	269	85.10%	13.00%	0.74%	1.12%	NA
Indica I	595	94.50%	1.80%	2.52%	1.18%	NA
Indica II	465	94.40%	5.60%	0.00%	0.00%	NA
Indica III	913	96.40%	2.00%	0.33%	1.31%	NA
Indica Intermediate	786	89.80%	6.00%	1.65%	2.54%	NA
Temperate Japonica	767	0.30%	99.60%	0.13%	0.00%	NA
Tropical Japonica	504	0.40%	99.60%	0.00%	0.00%	NA
Japonica Intermediate	241	1.20%	98.80%	0.00%	0.00%	NA
VI/Aromatic	96	3.10%	94.80%	1.04%	1.04%	NA
Intermediate	90	43.30%	55.60%	1.11%	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
vg0706750728	C -> DEL	N	N	silent_mutation	Average:25.663; most accessible tissue: Zhenshan97 panicle, score: 39.652	N	N	N	N
vg0706750728	C -> T	LOC_Os07g12080.1	upstream_gene_variant ; 4384.0bp to feature; MODIFIER	silent_mutation	Average:25.663; most accessible tissue: Zhenshan97 panicle, score: 39.652	N	N	N	N
vg0706750728	C -> T	LOC_Os07g12090.1	upstream_gene_variant ; 3565.0bp to feature; MODIFIER	silent_mutation	Average:25.663; most accessible tissue: Zhenshan97 panicle, score: 39.652	N	N	N	N
vg0706750728	C -> T	LOC_Os07g12100.1	intron_variant ; MODIFIER	silent_mutation	Average:25.663; 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
vg0706750728	NA	5.32E-30	mr1107	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
vg0706750728	NA	3.42E-07	mr1107	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
vg0706750728	NA	1.06E-12	mr1170	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
vg0706750728	NA	6.88E-36	mr1082_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
vg0706750728	2.70E-07	NA	mr1082_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
vg0706750728	NA	8.41E-32	mr1083_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
vg0706750728	1.30E-06	NA	mr1083_2	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
vg0706750728	NA	2.72E-32	mr1085_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
vg0706750728	7.97E-06	NA	mr1128_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
vg0706750728	NA	2.18E-44	mr1145_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
vg0706750728	2.23E-06	NA	mr1145_2	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
vg0706750728	NA	1.67E-35	mr1155_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
vg0706750728	NA	6.23E-08	mr1212_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
vg0706750728	NA	2.37E-12	mr1216_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
vg0706750728	NA	2.99E-24	mr1233_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
vg0706750728	NA	3.21E-40	mr1264_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
vg0706750728	NA	8.32E-08	mr1408_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
vg0706750728	NA	5.96E-17	mr1592_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
vg0706750728	NA	2.32E-22	mr1609_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
vg0706750728	NA	3.08E-06	mr1620_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
vg0706750728	NA	3.88E-09	mr1705_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
vg0706750728	NA	9.10E-07	mr1727_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
vg0706750728	NA	2.13E-07	mr1804_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
vg0706750728	NA	2.50E-07	mr1915_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
vg0706750728	NA	6.29E-09	mr1947_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