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Detailed information for vg0905696336:

Variant ID: vg0905696336 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 5696336
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.91, T: 0.09, others allele: 0.00, population size: 81. )

Flanking Sequence (100 bp) in Reference Genome:

CGGGCTCATCGGGCTCGGCCTCGAAACCCGGAGGGAAAGGAGGGATATCAATATGGTGGTCCTCATGATACCGCGCCTTGAGGTACTTGACGTCATGAGC[C/T]
GTTTTCTTCGCCGGATTCCGCAATCGGCGGTTCTTTTTAGCCTCCGCGGAGCAAAGGCCAAAAAGAGTCCGCAAAATGCGGAATAAGGGAGACGGCTCAC

Reverse complement sequence

GTGAGCCGTCTCCCTTATTCCGCATTTTGCGGACTCTTTTTGGCCTTTGCTCCGCGGAGGCTAAAAAGAACCGCCGATTGCGGAATCCGGCGAAGAAAAC[G/A]
GCTCATGACGTCAAGTACCTCAAGGCGCGGTATCATGAGGACCACCATATTGATATCCCTCCTTTCCCTCCGGGTTTCGAGGCCGAGCCCGATGAGCCCG

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	86.40%	7.00%	0.36%	6.24%	NA
All Indica	2759	93.00%	6.90%	0.07%	0.04%	NA
All Japonica	1512	83.80%	0.10%	0.46%	15.61%	NA
Aus	269	50.20%	48.30%	1.49%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	80.60%	19.10%	0.22%	0.00%	NA
Indica III	913	93.90%	6.10%	0.00%	0.00%	NA
Indica Intermediate	786	93.90%	5.90%	0.13%	0.13%	NA
Temperate Japonica	767	93.50%	0.10%	0.13%	6.26%	NA
Tropical Japonica	504	82.90%	0.20%	0.60%	16.27%	NA
Japonica Intermediate	241	54.80%	0.00%	1.24%	43.98%	NA
VI/Aromatic	96	32.30%	4.20%	4.17%	59.38%	NA
Intermediate	90	95.60%	3.30%	0.00%	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
vg0905696336	C -> DEL	LOC_Os09g10420.1	N	frameshift_variant	Average:65.816; most accessible tissue: Minghui63 flag leaf, score: 82.75	N	N	N	N
vg0905696336	C -> T	LOC_Os09g10420.1	synonymous_variant ; p.Thr320Thr; LOW	synonymous_codon	Average:65.816; most accessible tissue: Minghui63 flag leaf, score: 82.75	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0905696336	NA	8.96E-06	mr1036	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
vg0905696336	NA	8.99E-06	mr1174	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
vg0905696336	NA	6.91E-07	mr1188	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
vg0905696336	NA	8.92E-06	mr1330	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
vg0905696336	NA	9.11E-06	mr1332	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
vg0905696336	NA	2.10E-06	mr1347	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
vg0905696336	NA	1.55E-06	mr1787	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
vg0905696336	NA	6.91E-06	mr1906	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
vg0905696336	1.71E-06	9.79E-10	mr1939	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