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Detailed information for vg0316147114:

Variant ID: vg0316147114 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 16147114
Reference Allele: C	Alternative Allele: G
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTTTTTTAATTGGATGTGACTACACAGCTAGTGGTAGCTAGTTTGTACTCCATTTAGTATCTCCTTTCAACTTGAAAAATACAATAGTATCTTCTTTTCT[C/G]
ATTCTACATGAAAAACAAAAGTGAAAGGAAAAAAACAATCGATGATTAAACAGATTTATAGAGAGTTACTTTTGAACCATGCAAAAGTTACTTCCAATTA

Reverse complement sequence

TAATTGGAAGTAACTTTTGCATGGTTCAAAAGTAACTCTCTATAAATCTGTTTAATCATCGATTGTTTTTTTCCTTTCACTTTTGTTTTTCATGTAGAAT[G/C]
AGAAAAGAAGATACTATTGTATTTTTCAAGTTGAAAGGAGATACTAAATGGAGTACAAACTAGCTACCACTAGCTGTGTAGTCACATCCAATTAAAAAAA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	94.50%	4.90%	0.53%	0.11%	NA
All Indica	2759	97.30%	2.50%	0.18%	0.00%	NA
All Japonica	1512	99.30%	0.10%	0.33%	0.33%	NA
Aus	269	38.30%	56.90%	4.83%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	96.20%	3.50%	0.33%	0.00%	NA
Indica Intermediate	786	95.00%	4.70%	0.25%	0.00%	NA
Temperate Japonica	767	98.70%	0.10%	0.65%	0.52%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.00%	0.00%	0.41%	NA
VI/Aromatic	96	95.80%	3.10%	1.04%	0.00%	NA
Intermediate	90	92.20%	6.70%	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
vg0316147114	C -> DEL	N	N	silent_mutation	Average:16.104; most accessible tissue: Minghui63 flag leaf, score: 23.047	N	N	N	N
vg0316147114	C -> G	LOC_Os03g28090.1	upstream_gene_variant ; 4110.0bp to feature; MODIFIER	silent_mutation	Average:16.104; most accessible tissue: Minghui63 flag leaf, score: 23.047	N	N	N	N
vg0316147114	C -> G	LOC_Os03g28080-LOC_Os03g28090	intergenic_region ; MODIFIER	silent_mutation	Average:16.104; most accessible tissue: Minghui63 flag leaf, score: 23.047	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0316147114	NA	1.44E-15	mr1113	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
vg0316147114	4.43E-06	1.56E-20	mr1114	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
vg0316147114	1.54E-06	1.16E-18	mr1116	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
vg0316147114	6.69E-06	4.70E-21	mr1117	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
vg0316147114	2.76E-07	NA	mr1118	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
vg0316147114	NA	4.20E-17	mr1119	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
vg0316147114	5.92E-09	3.12E-28	mr1123	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
vg0316147114	NA	5.00E-18	mr1240	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
vg0316147114	6.60E-09	1.25E-22	mr1242	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
vg0316147114	4.79E-06	9.60E-23	mr1247	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
vg0316147114	3.88E-06	1.69E-16	mr1496	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
vg0316147114	2.32E-07	1.44E-28	mr1858	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
vg0316147114	2.22E-07	1.32E-28	mr1859	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
vg0316147114	4.95E-07	1.46E-20	mr1113_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
vg0316147114	1.20E-06	5.75E-19	mr1114_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
vg0316147114	3.08E-06	2.19E-20	mr1117_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
vg0316147114	3.35E-07	NA	mr1118_2	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
vg0316147114	1.32E-06	1.26E-19	mr1119_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
vg0316147114	1.21E-08	2.31E-25	mr1123_2	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
vg0316147114	1.76E-07	2.60E-21	mr1240_2	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
vg0316147114	9.09E-09	NA	mr1242_2	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
vg0316147114	8.65E-07	9.74E-24	mr1247_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
vg0316147114	2.31E-06	NA	mr1495_2	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
vg0316147114	1.29E-07	2.03E-15	mr1496_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
vg0316147114	5.57E-07	9.03E-18	mr1936_2	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
vg0316147114	NA	2.33E-16	mr1961_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