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Detailed information for vg0906477614:

Variant ID: vg0906477614 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 6477614
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 72. )

Flanking Sequence (100 bp) in Reference Genome:

GGAAACCATCTGATATAGATCCTTCTGGAAAGGACTCTGATCCGGCTAATATGGAAACAAGTTCTTCCAAAGAAACCGGGCCGACTGCTGAGGATCATCC[G/A]
AGTGACAATCAGCTGGCAACCGATAATGTAGAATCCAGCAATCAACCCCCGACCGGAAACCAGTTTGCCGAAGCTGAAGCCAGAGTCAATCAGGAGCCCC

Reverse complement sequence

GGGGCTCCTGATTGACTCTGGCTTCAGCTTCGGCAAACTGGTTTCCGGTCGGGGGTTGATTGCTGGATTCTACATTATCGGTTGCCAGCTGATTGTCACT[C/T]
GGATGATCCTCAGCAGTCGGCCCGGTTTCTTTGGAAGAACTTGTTTCCATATTAGCCGGATCAGAGTCCTTTCCAGAAGGATCTATATCAGATGGTTTCC

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	46.30%	10.70%	1.86%	41.16%	NA
All Indica	2759	22.10%	7.00%	2.54%	68.39%	NA
All Japonica	1512	98.30%	0.40%	0.20%	1.12%	NA
Aus	269	11.90%	79.60%	2.60%	5.95%	NA
Indica I	595	32.90%	0.70%	1.51%	64.87%	NA
Indica II	465	15.90%	9.00%	3.87%	71.18%	NA
Indica III	913	14.50%	8.70%	1.86%	75.03%	NA
Indica Intermediate	786	26.30%	8.70%	3.31%	61.70%	NA
Temperate Japonica	767	99.60%	0.00%	0.13%	0.26%	NA
Tropical Japonica	504	99.20%	0.40%	0.00%	0.40%	NA
Japonica Intermediate	241	92.10%	1.70%	0.83%	5.39%	NA
VI/Aromatic	96	5.20%	87.50%	4.17%	3.12%	NA
Intermediate	90	60.00%	11.10%	4.44%	24.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0906477614	G -> DEL	LOC_Os09g11600.1	N	frameshift_variant	Average:29.389; most accessible tissue: Minghui63 young leaf, score: 57.221	N	N	N	N
vg0906477614	G -> A	LOC_Os09g11600.1	synonymous_variant ; p.Pro413Pro; LOW	synonymous_codon	Average:29.389; most accessible tissue: Minghui63 young leaf, score: 57.221	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0906477614	2.81E-06	1.04E-09	mr1310	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
vg0906477614	NA	1.22E-13	mr1498	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
vg0906477614	NA	2.06E-06	mr1570	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
vg0906477614	NA	1.08E-10	mr1769	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
vg0906477614	NA	7.65E-07	mr1803	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
vg0906477614	NA	3.69E-06	mr1830	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
vg0906477614	NA	5.26E-08	mr1925	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
vg0906477614	NA	1.25E-08	mr1951	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
vg0906477614	1.07E-06	3.33E-11	mr1310_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
vg0906477614	NA	2.91E-12	mr1498_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
vg0906477614	NA	1.84E-13	mr1769_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
vg0906477614	NA	5.34E-08	mr1925_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
vg0906477614	NA	3.71E-10	mr1951_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