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Detailed information for vg0335384067:

Variant ID: vg0335384067 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 35384067
Reference Allele: G	Alternative Allele: C,A
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.76, C: 0.24, others allele: 0.00, population size: 173. )

Flanking Sequence (100 bp) in Reference Genome:

TGAGTGTTTCATGAATGATTGAAGGCAAAACTCTCTCATTGAAATTCTCCCCCAGGGACCTGTAGATGGTTGGTAGCTTCTCTGGTAACGGTCTTGTAAG[G/C,A]
ACACGAAGACCAATTCTCACCTGTCCAAGTTATCAAATTGTATCAAACTAAAAATGTGTTGGTACTGACCTCTACCAATGTTACTTTGAAGCAAAGGTCT

Reverse complement sequence

AGACCTTTGCTTCAAAGTAACATTGGTAGAGGTCAGTACCAACACATTTTTAGTTTGATACAATTTGATAACTTGGACAGGTGAGAATTGGTCTTCGTGT[C/G,T]
CTTACAAGACCGTTACCAGAGAAGCTACCAACCATCTACAGGTCCCTGGGGGAGAATTTCAATGAGAGAGTTTTGCCTTCAATCATTCATGAAACACTCA

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	76.90%	23.00%	0.11%	0.00%	NA
All Indica	2759	90.10%	9.90%	0.00%	0.00%	NA
All Japonica	1512	47.40%	52.30%	0.33%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	99.50%	0.50%	0.00%	0.00%	NA
Indica II	465	87.10%	12.90%	0.00%	0.00%	NA
Indica III	913	86.50%	13.50%	0.00%	0.00%	NA
Indica Intermediate	786	88.90%	11.10%	0.00%	0.00%	NA
Temperate Japonica	767	11.20%	88.10%	0.65%	0.00%	NA
Tropical Japonica	504	93.30%	6.70%	0.00%	0.00%	NA
Japonica Intermediate	241	66.40%	33.60%	0.00%	0.00%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	78.90%	21.10%	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
vg0335384067	G -> C	LOC_Os03g62490.1	synonymous_variant ; p.Val105Val; LOW	synonymous_codon	Average:47.873; most accessible tissue: Callus, score: 59.804	N	N	N	N
vg0335384067	G -> A	LOC_Os03g62490.1	synonymous_variant ; p.Val105Val; LOW	N	Average:47.873; most accessible tissue: Callus, score: 59.804	N	N	N	N
vg0335384067	G -> A	LOC_Os03g62480.1	upstream_gene_variant ; 2086.0bp to feature; MODIFIER	N	Average:47.873; most accessible tissue: Callus, score: 59.804	N	N	N	N
vg0335384067	G -> A	LOC_Os03g62500.1	downstream_gene_variant ; 1715.0bp to feature; MODIFIER	N	Average:47.873; most accessible tissue: Callus, score: 59.804	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0335384067	5.15E-06	NA	Awn_length	Ind_All	YES	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0335384067	NA	5.74E-25	mr1115_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
vg0335384067	4.15E-06	4.39E-07	mr1117_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
vg0335384067	1.16E-06	1.69E-07	mr1119_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
vg0335384067	3.48E-07	NA	mr1123_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
vg0335384067	NA	5.38E-07	mr1180_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
vg0335384067	NA	7.66E-07	mr1183_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
vg0335384067	NA	1.70E-06	mr1229_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
vg0335384067	NA	5.15E-06	mr1232_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
vg0335384067	NA	7.92E-06	mr1233_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
vg0335384067	NA	8.71E-06	mr1247_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
vg0335384067	NA	6.76E-07	mr1252_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
vg0335384067	NA	9.52E-07	mr1554_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
vg0335384067	NA	2.77E-06	mr1730_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
vg0335384067	NA	9.24E-08	mr1748_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
vg0335384067	NA	2.69E-08	mr1794_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