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Detailed information for vg0327747214:

Variant ID: vg0327747214 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 27747214
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GTTCGTCGCCAACTTCCAAGGAACTTACAAGCGCCACGCGATTGAAGACGACCTACATGCGTTGACACAGAACCCGGGTGAATCCTTGAGTGATTATGTT[T/C]
GGCGCTTTAATGAGTGCAGAAATACAATCCCCGAAATCACCGACGCTTCTGTAATCCGCGCCTTCAAGTCCGGTGTCAGAGATCGCTATACTACCCAGGA

Reverse complement sequence

TCCTGGGTAGTATAGCGATCTCTGACACCGGACTTGAAGGCGCGGATTACAGAAGCGTCGGTGATTTCGGGGATTGTATTTCTGCACTCATTAAAGCGCC[A/G]
AACATAATCACTCAAGGATTCACCCGGGTTCTGTGTCAACGCATGTAGGTCGTCTTCAATCGCGTGGCGCTTGTAAGTTCCTTGGAAGTTGGCGACGAAC

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	60.90%	38.90%	0.15%	0.08%	NA
All Indica	2759	90.40%	9.30%	0.22%	0.14%	NA
All Japonica	1512	2.60%	97.40%	0.00%	0.00%	NA
Aus	269	98.10%	1.90%	0.00%	0.00%	NA
Indica I	595	93.60%	5.40%	0.84%	0.17%	NA
Indica II	465	96.60%	3.20%	0.00%	0.22%	NA
Indica III	913	86.60%	13.40%	0.00%	0.00%	NA
Indica Intermediate	786	88.50%	11.10%	0.13%	0.25%	NA
Temperate Japonica	767	0.40%	99.60%	0.00%	0.00%	NA
Tropical Japonica	504	6.30%	93.70%	0.00%	0.00%	NA
Japonica Intermediate	241	2.10%	97.90%	0.00%	0.00%	NA
VI/Aromatic	96	38.50%	61.50%	0.00%	0.00%	NA
Intermediate	90	47.80%	51.10%	1.11%	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
vg0327747214	T -> C	LOC_Os03g48674.1	missense_variant ; p.Trp452Arg; MODERATE	nonsynonymous_codon ; W452Q	Average:36.842; most accessible tissue: Minghui63 panicle, score: 50.413	benign	-0.047	TOLERATED	0.64
vg0327747214	T -> C	LOC_Os03g48674.1	missense_variant ; p.Trp452Arg; MODERATE	nonsynonymous_codon ; W452R	Average:36.842; most accessible tissue: Minghui63 panicle, score: 50.413	benign	-0.417	TOLERATED	1.00
vg0327747214	T -> DEL	LOC_Os03g48674.1	N	frameshift_variant	Average:36.842; most accessible tissue: Minghui63 panicle, score: 50.413	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0327747214	NA	2.88E-06	Awn_length	Ind_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
vg0327747214	NA	5.76E-12	mr1579	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
vg0327747214	NA	6.33E-26	mr1632	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
vg0327747214	1.09E-06	1.56E-125	mr1750	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
vg0327747214	NA	4.18E-07	mr1750	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
vg0327747214	NA	2.97E-39	mr1873	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
vg0327747214	1.92E-09	2.82E-164	mr1750_2	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