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Detailed information for vg0900606284:

Variant ID: vg0900606284 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 606284
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 130. )

Flanking Sequence (100 bp) in Reference Genome:

AATCTGAGTTTCGCACCCTAGCTCCGAACATCTCTCTACCCATCCCTGATTTGTCCATGTACCATTGATGGAACCGGTACATCTGTGTAGGTAGCTCTCT[G/A]
ATCTTATCAGGCGTGACTAGCAGTTCACCGAGTTTAAACGTGTACATGACCGGAGCCGTTTCGATAGGTGCGTCCTCTAGCAACTGCTCCATACTCAGTC

Reverse complement sequence

GACTGAGTATGGAGCAGTTGCTAGAGGACGCACCTATCGAAACGGCTCCGGTCATGTACACGTTTAAACTCGGTGAACTGCTAGTCACGCCTGATAAGAT[C/T]
AGAGAGCTACCTACACAGATGTACCGGTTCCATCAATGGTACATGGACAAATCAGGGATGGGTAGAGAGATGTTCGGAGCTAGGGTGCGAAACTCAGATT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	72.80%	21.30%	0.66%	5.23%	NA
All Indica	2759	62.70%	36.30%	0.91%	0.04%	NA
All Japonica	1512	83.40%	0.10%	0.33%	16.20%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	67.10%	31.90%	0.84%	0.17%	NA
Indica II	465	83.00%	16.30%	0.65%	0.00%	NA
Indica III	913	50.30%	48.70%	0.99%	0.00%	NA
Indica Intermediate	786	62.00%	37.00%	1.02%	0.00%	NA
Temperate Japonica	767	70.50%	0.10%	0.13%	29.20%	NA
Tropical Japonica	504	99.80%	0.00%	0.20%	0.00%	NA
Japonica Intermediate	241	90.00%	0.00%	1.24%	8.71%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	93.30%	4.40%	1.11%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0900606284	G -> DEL	LOC_Os09g01900.1	N	frameshift_variant	Average:35.145; most accessible tissue: Zhenshan97 flag leaf, score: 70.837	N	N	N	N
vg0900606284	G -> A	LOC_Os09g01900.1	synonymous_variant ; p.Ile597Ile; LOW	synonymous_codon	Average:35.145; most accessible tissue: Zhenshan97 flag leaf, score: 70.837	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0900606284	NA	1.81E-07	mr1086	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
vg0900606284	NA	7.78E-07	mr1088	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
vg0900606284	5.47E-06	1.59E-07	mr1103	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
vg0900606284	NA	2.83E-08	mr1104	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
vg0900606284	NA	1.15E-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
vg0900606284	NA	4.49E-06	mr1131	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
vg0900606284	1.95E-06	NA	mr1213	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
vg0900606284	1.55E-07	9.06E-12	mr1213	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
vg0900606284	NA	7.04E-06	mr1224	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
vg0900606284	NA	1.58E-08	mr1246	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
vg0900606284	NA	8.97E-06	mr1336	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
vg0900606284	NA	3.93E-06	mr1404	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
vg0900606284	3.94E-06	1.09E-07	mr1620	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
vg0900606284	NA	2.44E-06	mr1246_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