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Detailed information for vg0141986897:

Variant ID: vg0141986897 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 41986897
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.01, others allele: 0.00, population size: 222. )

Flanking Sequence (100 bp) in Reference Genome:

ACTGTCCAAGATTAAGGGGAACATTCTCAAGCCGAAAACATCCATCAAGGTAGAGATTCCTAAGGCTTTTCATTTTTCTCAAGTCTTTTGGGAGCTGTTT[C/T]
AAGTAACAACACTCTGAGAGTCTTAGAGTTTGCAGATTGTAGAGATATACAACATCATCTGGAATAGATGTGATCCAACTGTTGGAGAGGTCAAGATACC

Reverse complement sequence

GGTATCTTGACCTCTCCAACAGTTGGATCACATCTATTCCAGATGATGTTGTATATCTCTACAATCTGCAAACTCTAAGACTCTCAGAGTGTTGTTACTT[G/A]
AAACAGCTCCCAAAAGACTTGAGAAAAATGAAAAGCCTTAGGAATCTCTACCTTGATGGATGTTTTCGGCTTGAGAATGTTCCCCTTAATCTTGGACAGT

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	80.50%	5.70%	0.55%	13.27%	NA
All Indica	2759	69.60%	9.30%	0.80%	20.33%	NA
All Japonica	1512	95.60%	0.30%	0.26%	3.77%	NA
Aus	269	98.90%	0.40%	0.00%	0.74%	NA
Indica I	595	57.60%	13.30%	1.18%	27.90%	NA
Indica II	465	88.40%	2.40%	0.43%	8.82%	NA
Indica III	913	65.90%	11.50%	0.33%	22.23%	NA
Indica Intermediate	786	71.60%	7.90%	1.27%	19.21%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	87.30%	0.80%	0.60%	11.31%	NA
Japonica Intermediate	241	99.20%	0.40%	0.41%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	86.70%	5.60%	0.00%	7.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0141986897	C -> T	LOC_Os01g72390.1	synonymous_variant ; p.Leu585Leu; LOW	synonymous_codon	Average:49.583; most accessible tissue: Minghui63 flower, score: 77.024	N	N	N	N
vg0141986897	C -> DEL	LOC_Os01g72390.1	N	frameshift_variant	Average:49.583; most accessible tissue: Minghui63 flower, score: 77.024	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0141986897	NA	3.04E-06	mr1024	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
vg0141986897	NA	6.02E-06	mr1128	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
vg0141986897	5.74E-07	6.83E-10	mr1336	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
vg0141986897	NA	2.81E-06	mr1715	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
vg0141986897	2.61E-08	1.00E-07	mr1719	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