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Detailed information for vg0901243062:

Variant ID: vg0901243062 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 1243062
Reference Allele: C	Alternative Allele: G
Primary Allele: G	Secondary Allele: C

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, C: 0.00, others allele: 0.00, population size: 354. )

Flanking Sequence (100 bp) in Reference Genome:

ATAATGACAATCCATAAACAAGTGTTGGATCGTCTCATTTTTCATGCAAAAACAACATGTTAAACCCCCATTCCAATTCCGTCGTGCAAGATTATCCTTT[C/G]
TTAAGACGACTCCCTTGAGCAAATACCACATAAAGATCTTGATCTTAAGCGGCATCTTAAGCTTCCAAATGAACTTATTTCTATCAATGTAACCATTGCT

Reverse complement sequence

AGCAATGGTTACATTGATAGAAATAAGTTCATTTGGAAGCTTAAGATGCCGCTTAAGATCAAGATCTTTATGTGGTATTTGCTCAAGGGAGTCGTCTTAA[G/C]
AAAGGATAATCTTGCACGACGGAATTGGAATGGGGGTTTAACATGTTGTTTTTGCATGAAAAATGAGACGATCCAACACTTGTTTATGGATTGTCATTAT

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	77.20%	18.70%	1.08%	3.00%	NA
All Indica	2759	96.80%	2.50%	0.11%	0.51%	NA
All Japonica	1512	35.70%	52.80%	3.11%	8.33%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	95.30%	3.40%	0.17%	1.18%	NA
Indica II	465	99.10%	0.60%	0.00%	0.22%	NA
Indica III	913	98.20%	1.80%	0.00%	0.00%	NA
Indica Intermediate	786	95.00%	3.90%	0.25%	0.76%	NA
Temperate Japonica	767	3.00%	82.90%	3.91%	10.17%	NA
Tropical Japonica	504	78.40%	14.10%	1.39%	6.15%	NA
Japonica Intermediate	241	50.60%	38.20%	4.15%	7.05%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	82.20%	14.40%	1.11%	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
vg0901243062	C -> G	LOC_Os09g02729.1	upstream_gene_variant ; 4529.0bp to feature; MODIFIER	silent_mutation	Average:51.182; most accessible tissue: Zhenshan97 panicle, score: 61.671	N	N	N	N
vg0901243062	C -> G	LOC_Os09g02729.2	upstream_gene_variant ; 4529.0bp to feature; MODIFIER	silent_mutation	Average:51.182; most accessible tissue: Zhenshan97 panicle, score: 61.671	N	N	N	N
vg0901243062	C -> G	LOC_Os09g02750.1	intron_variant ; MODIFIER	silent_mutation	Average:51.182; most accessible tissue: Zhenshan97 panicle, score: 61.671	N	N	N	N
vg0901243062	C -> DEL	N	N	silent_mutation	Average:51.182; most accessible tissue: Zhenshan97 panicle, score: 61.671	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0901243062	NA	2.57E-37	Grain_thickness	All	Not	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
vg0901243062	NA	2.29E-14	Grain_thickness	Jap_All	Not	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
vg0901243062	1.69E-08	1.14E-54	Grain_width	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
vg0901243062	NA	6.23E-13	Grain_width	Jap_All	Not	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
vg0901243062	NA	2.33E-07	mr1916	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
vg0901243062	NA	4.95E-07	mr1551_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
vg0901243062	NA	1.96E-10	mr1552_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
vg0901243062	NA	1.26E-07	mr1578_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
vg0901243062	NA	4.50E-19	mr1980_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