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Detailed information for vg0321595057:

Variant ID: vg0321595057 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 21595057
Reference Allele: C	Alternative Allele: G
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CGATCGGGAGAGCAGGTCTCTGGAACATTCGTCTTCGATGTCCTGCACCGGGAGAAGGTGACAATAAGGTTTTTGGAAGCGCTTCGCGCGACTGCTCCCT[C/G]
TTCGCTTGCGTGCTGTGCGCCATCATCAACGCCCGCAACCGCGAGTACTTCCTACCAGTGGCGGACCTAGAAAAATTGCACTGGGTGTGCCCATTCTAGC

Reverse complement sequence

GCTAGAATGGGCACACCCAGTGCAATTTTTCTAGGTCCGCCACTGGTAGGAAGTACTCGCGGTTGCGGGCGTTGATGATGGCGCACAGCACGCAAGCGAA[G/C]
AGGGAGCAGTCGCGCGAAGCGCTTCCAAAAACCTTATTGTCACCTTCTCCCGGTGCAGGACATCGAAGACGAATGTTCCAGAGACCTGCTCTCCCGATCG

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	92.70%	3.40%	3.30%	0.61%	NA
All Indica	2759	88.10%	5.50%	5.33%	1.05%	NA
All Japonica	1512	99.90%	0.10%	0.00%	0.00%	NA
Aus	269	98.10%	0.70%	1.12%	0.00%	NA
Indica I	595	92.80%	2.40%	4.87%	0.00%	NA
Indica II	465	85.20%	5.80%	4.95%	4.09%	NA
Indica III	913	88.10%	7.90%	4.05%	0.00%	NA
Indica Intermediate	786	86.30%	5.10%	7.38%	1.27%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	94.80%	3.10%	2.08%	0.00%	NA
Intermediate	90	93.30%	2.20%	4.44%	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
vg0321595057	C -> DEL	N	N	silent_mutation	Average:61.337; most accessible tissue: Zhenshan97 panicle, score: 75.67	N	N	N	N
vg0321595057	C -> G	LOC_Os03g38870.1	upstream_gene_variant ; 4620.0bp to feature; MODIFIER	silent_mutation	Average:61.337; most accessible tissue: Zhenshan97 panicle, score: 75.67	N	N	N	N
vg0321595057	C -> G	LOC_Os03g38864-LOC_Os03g38870	intergenic_region ; MODIFIER	silent_mutation	Average:61.337; most accessible tissue: Zhenshan97 panicle, score: 75.67	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0321595057	9.45E-06	9.45E-06	mr1329	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
vg0321595057	1.44E-06	1.44E-06	mr1524	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