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Detailed information for vg0505523915:

Variant ID: vg0505523915 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 5523915
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 259. )

Flanking Sequence (100 bp) in Reference Genome:

GATTTAAGATCTTCTCCACATAATGGGACTGCAAGAGTGTAATCCCATTCTCACCTCTAATTAACTTAATGTTTAAGATAACATCAGCTACTCCCAAATC[C/T]
TTCATATCAAAATTTTGAGACAAGAATGATTTAACCTCATTTATCACCTCAAGGTTTGTCCCAAATATCAGTATGTCATCAACATACAAGCACAGAATAA

Reverse complement sequence

TTATTCTGTGCTTGTATGTTGATGACATACTGATATTTGGGACAAACCTTGAGGTGATAAATGAGGTTAAATCATTCTTGTCTCAAAATTTTGATATGAA[G/A]
GATTTGGGAGTAGCTGATGTTATCTTAAACATTAAGTTAATTAGAGGTGAGAATGGGATTACACTCTTGCAGTCCCATTATGTGGAGAAGATCTTAAATC

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	92.60%	4.40%	3.05%	0.02%	NA
All Indica	2759	98.50%	1.30%	0.22%	0.00%	NA
All Japonica	1512	90.80%	0.10%	8.99%	0.07%	NA
Aus	269	40.50%	59.50%	0.00%	0.00%	NA
Indica I	595	99.30%	0.30%	0.34%	0.00%	NA
Indica II	465	98.10%	1.90%	0.00%	0.00%	NA
Indica III	913	98.60%	1.10%	0.33%	0.00%	NA
Indica Intermediate	786	98.10%	1.80%	0.13%	0.00%	NA
Temperate Japonica	767	86.20%	0.00%	13.69%	0.13%	NA
Tropical Japonica	504	99.20%	0.00%	0.79%	0.00%	NA
Japonica Intermediate	241	88.00%	0.80%	11.20%	0.00%	NA
VI/Aromatic	96	93.80%	6.20%	0.00%	0.00%	NA
Intermediate	90	93.30%	4.40%	2.22%	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
vg0505523915	C -> T	LOC_Os05g09736.1	synonymous_variant ; p.Lys289Lys; LOW	synonymous_codon	Average:21.272; most accessible tissue: Minghui63 flower, score: 37.124	N	N	N	N
vg0505523915	C -> DEL	LOC_Os05g09736.1	N	frameshift_variant	Average:21.272; most accessible tissue: Minghui63 flower, score: 37.124	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0505523915	NA	5.70E-23	mr1123	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
vg0505523915	6.25E-06	NA	mr1242	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
vg0505523915	NA	5.91E-14	mr1496	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