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Detailed information for vg0918391108:

Variant ID: vg0918391108 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 18391108
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 313. )

Flanking Sequence (100 bp) in Reference Genome:

CCCTCGGAATTGCTCATGGGCAAGAGCCAGGTTTTCTAGATAACTTTGGTGGCATAGAGAGGTATCCTTACCAGCGTGGCGCTATCGGGACAGTGATCGG[C/T]
ATGCCAGGCACTCCTTCACCAATGCGCGGAATAACCAGAAGTAGCTTCCCTGCACCTCAGGAGCAGCCTTGGCGTCAAGAGAGATATATTATGGATCCAG

Reverse complement sequence

CTGGATCCATAATATATCTCTCTTGACGCCAAGGCTGCTCCTGAGGTGCAGGGAAGCTACTTCTGGTTATTCCGCGCATTGGTGAAGGAGTGCCTGGCAT[G/A]
CCGATCACTGTCCCGATAGCGCCACGCTGGTAAGGATACCTCTCTATGCCACCAAAGTTATCTAGAAAACCTGGCTCTTGCCCATGAGCAATTCCGAGGG

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	80.10%	19.30%	0.08%	0.53%	NA
All Indica	2759	66.10%	32.80%	0.14%	0.87%	NA
All Japonica	1512	99.90%	0.00%	0.00%	0.07%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	63.40%	35.60%	0.34%	0.67%	NA
Indica II	465	88.60%	10.50%	0.00%	0.86%	NA
Indica III	913	51.60%	47.20%	0.11%	1.10%	NA
Indica Intermediate	786	71.90%	27.20%	0.13%	0.76%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.00%	0.00%	0.41%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	95.60%	4.40%	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
vg0918391108	C -> DEL	LOC_Os09g30210.1	N	frameshift_variant	Average:69.25; most accessible tissue: Zhenshan97 panicle, score: 85.665	N	N	N	N
vg0918391108	C -> T	LOC_Os09g30210.1	synonymous_variant ; p.Gly478Gly; LOW	synonymous_codon	Average:69.25; most accessible tissue: Zhenshan97 panicle, score: 85.665	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0918391108	NA	2.52E-07	mr1557	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
vg0918391108	NA	4.34E-06	mr1944	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
vg0918391108	NA	9.87E-08	mr1970	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
vg0918391108	NA	7.69E-09	mr1973	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
vg0918391108	1.62E-07	NA	mr1557_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
vg0918391108	5.34E-07	2.33E-09	mr1557_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
vg0918391108	6.77E-06	NA	mr1598_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
vg0918391108	NA	3.08E-07	mr1970_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
vg0918391108	NA	1.91E-08	mr1973_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