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Detailed information for vg0922577989:

Variant ID: vg0922577989 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 22577989
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.51, C: 0.49, others allele: 0.00, population size: 70. )

Flanking Sequence (100 bp) in Reference Genome:

TAGTGACATGGCTAAATGATGGATCGAAGACCAAACCATGGATGGAGAGCGGATGGCAGGTCCAAGCATCTGCACCAGAGCGGTAGAGATGATCACCTCG[T/C]
TTGAAGGCGCTACAGAGCGCGGCGACGATGTAGGTGCCATCATCAAGGCAGCGCAGGATGCCAACCTGTTTGTCGATGAACCTGTTGTCGAGTTTCGGGG

Reverse complement sequence

CCCCGAAACTCGACAACAGGTTCATCGACAAACAGGTTGGCATCCTGCGCTGCCTTGATGATGGCACCTACATCGTCGCCGCGCTCTGTAGCGCCTTCAA[A/G]
CGAGGTGATCATCTCTACCGCTCTGGTGCAGATGCTTGGACCTGCCATCCGCTCTCCATCCATGGTTTGGTCTTCGATCCATCATTTAGCCATGTCACTA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	84.60%	15.10%	0.02%	0.23%	NA
All Indica	2759	74.40%	25.20%	0.04%	0.40%	NA
All Japonica	1512	99.70%	0.30%	0.00%	0.00%	NA
Aus	269	95.90%	4.10%	0.00%	0.00%	NA
Indica I	595	68.40%	30.90%	0.17%	0.50%	NA
Indica II	465	80.20%	19.60%	0.00%	0.22%	NA
Indica III	913	77.10%	22.20%	0.00%	0.66%	NA
Indica Intermediate	786	72.40%	27.50%	0.00%	0.13%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.80%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	93.30%	6.70%	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
vg0922577989	T -> DEL	LOC_Os09g39280.1	N	frameshift_variant	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0922577989	T -> C	LOC_Os09g39280.1	synonymous_variant ; p.Lys141Lys; LOW	synonymous_codon	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0922577989	NA	2.91E-06	mr1344	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
vg0922577989	NA	4.98E-06	mr1397	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
vg0922577989	NA	4.56E-06	mr1625	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
vg0922577989	2.05E-08	NA	mr1865	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
vg0922577989	1.24E-09	4.15E-12	mr1865	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
vg0922577989	4.44E-06	NA	mr1865_2	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
vg0922577989	1.66E-06	6.74E-09	mr1865_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