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Detailed information for vg0321154919:

Variant ID: vg0321154919 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 21154919
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: 254. )

Flanking Sequence (100 bp) in Reference Genome:

GCTTATGCAATTACTCTATGTCATGACGATGATATTACTCTCGAAGTTCTTCCCGATGGGCAAAACCGACGCCCTTTGTGGACGAATTTCCAGTTTCCAG[C/T]
AGACAAGGGACGAGTCCATTCCGGAAGCATGGGAACTACTGCAGGAGTACGTGGCCGCCTGTCCTCATCATGGAATGGACGACTGGCTGATCTTGCAGAA

Reverse complement sequence

TTCTGCAAGATCAGCCAGTCGTCCATTCCATGATGAGGACAGGCGGCCACGTACTCCTGCAGTAGTTCCCATGCTTCCGGAATGGACTCGTCCCTTGTCT[G/A]
CTGGAAACTGGAAATTCGTCCACAAAGGGCGTCGGTTTTGCCCATCGGGAAGAACTTCGAGAGTAATATCATCGTCATGACATAGAGTAATTGCATAAGC

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	56.20%	42.80%	0.78%	0.15%	NA
All Indica	2759	26.70%	71.70%	1.34%	0.22%	NA
All Japonica	1512	99.20%	0.80%	0.00%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	75.80%	23.20%	0.67%	0.34%	NA
Indica II	465	9.70%	87.10%	2.80%	0.43%	NA
Indica III	913	7.30%	91.50%	0.99%	0.22%	NA
Indica Intermediate	786	22.30%	76.30%	1.40%	0.00%	NA
Temperate Japonica	767	99.60%	0.40%	0.00%	0.00%	NA
Tropical Japonica	504	98.40%	1.60%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	96.90%	3.10%	0.00%	0.00%	NA
Intermediate	90	65.60%	33.30%	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
vg0321154919	C -> T	LOC_Os03g38100.1	stop_gained ; p.Gln16*; HIGH	stop_gained	Average:48.689; most accessible tissue: Minghui63 flag leaf, score: 72.472	N	N	N	N
vg0321154919	C -> DEL	LOC_Os03g38100.1	N	frameshift_variant	Average:48.689; most accessible tissue: Minghui63 flag leaf, score: 72.472	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0321154919	NA	1.54E-13	Grain_length	All	Not	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0321154919	NA	7.52E-06	mr1046	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
vg0321154919	NA	2.82E-06	mr1057	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
vg0321154919	NA	5.87E-07	mr1058	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
vg0321154919	NA	2.93E-06	mr1221	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
vg0321154919	NA	8.44E-06	mr1568	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
vg0321154919	NA	9.21E-09	mr1637	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
vg0321154919	NA	3.93E-09	mr1663	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
vg0321154919	NA	4.81E-08	mr1666	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
vg0321154919	NA	2.18E-08	mr1669	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
vg0321154919	NA	9.63E-06	mr1727	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
vg0321154919	NA	2.26E-09	mr1804	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
vg0321154919	NA	8.78E-07	mr1928	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
vg0321154919	4.85E-06	4.85E-06	mr1978	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