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Detailed information for vg0902200100:

Variant ID: vg0902200100 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 2200100
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.97, A: 0.03, others allele: 0.00, population size: 78. )

Flanking Sequence (100 bp) in Reference Genome:

CTATTGGGATAACTTATGACTCATTATTTAATGATGGTTTAATGATAGTTCACGATGGTTAATCGTGATTGGTTAATTAATTACTTGCCAACTAAAATTT[A/G]
ATAATGGTGGGTTGTGAGCACATGGTTTTGAGAGTCGTGCTCATGACAATTAAGGACCGGTTCGCGAGCTTCTATTGTGAAACATTAACCGTGCCAACCA

Reverse complement sequence

TGGTTGGCACGGTTAATGTTTCACAATAGAAGCTCGCGAACCGGTCCTTAATTGTCATGAGCACGACTCTCAAAACCATGTGCTCACAACCCACCATTAT[T/C]
AAATTTTAGTTGGCAAGTAATTAATTAACCAATCACGATTAACCATCGTGAACTATCATTAAACCATCATTAAATAATGAGTCATAAGTTATCCCAATAG

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	22.70%	0.30%	35.91%	41.16%	NA
All Indica	2759	3.00%	0.10%	44.00%	52.88%	NA
All Japonica	1512	64.00%	0.00%	9.39%	26.65%	NA
Aus	269	0.40%	2.20%	95.54%	1.86%	NA
Indica I	595	5.50%	0.00%	32.77%	61.68%	NA
Indica II	465	2.80%	0.00%	50.75%	46.45%	NA
Indica III	913	1.00%	0.00%	41.51%	57.50%	NA
Indica Intermediate	786	3.40%	0.50%	51.40%	44.66%	NA
Temperate Japonica	767	96.90%	0.00%	0.91%	2.22%	NA
Tropical Japonica	504	20.20%	0.00%	21.03%	58.73%	NA
Japonica Intermediate	241	50.60%	0.00%	12.03%	37.34%	NA
VI/Aromatic	96	1.00%	3.10%	56.25%	39.58%	NA
Intermediate	90	22.20%	0.00%	33.33%	44.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0902200100	A -> G	LOC_Os09g04170.1	downstream_gene_variant ; 2356.0bp to feature; MODIFIER	silent_mutation	Average:38.76; most accessible tissue: Zhenshan97 flag leaf, score: 72.387	N	N	N	N
vg0902200100	A -> G	LOC_Os09g04170-LOC_Os09g04190	intergenic_region ; MODIFIER	silent_mutation	Average:38.76; most accessible tissue: Zhenshan97 flag leaf, score: 72.387	N	N	N	N
vg0902200100	A -> DEL	N	N	silent_mutation	Average:38.76; most accessible tissue: Zhenshan97 flag leaf, score: 72.387	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0902200100	NA	3.56E-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
vg0902200100	NA	1.29E-12	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
vg0902200100	NA	1.49E-15	mr1301	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
vg0902200100	NA	4.32E-09	mr1533	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
vg0902200100	NA	6.15E-06	mr1942	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
vg0902200100	NA	4.19E-09	mr1993	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
vg0902200100	NA	5.23E-06	mr1159_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
vg0902200100	NA	2.49E-06	mr1277_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
vg0902200100	NA	3.80E-08	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
vg0902200100	3.12E-06	9.87E-07	mr1636_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