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Detailed information for vg0334406362:

Variant ID: vg0334406362 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 34406362
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCCCTTTTGTAATGCAGTTGTGAGATCGGGATCTGTCCGCAGCCCAACATGACTGTACATCTACTCTATAATAAAGAGACCTCTGTTGCTGTGATAATCT[G/A]
TCTTCCTGTGATATCAGCACTGTGTCCTGGGACTGGTATCGATTAACAGGTTAAATTGGAGCGTCACGGGCTAGTTCCGGTCGGTACTAGTTCGGGGCGT

Reverse complement sequence

ACGCCCCGAACTAGTACCGACCGGAACTAGCCCGTGACGCTCCAATTTAACCTGTTAATCGATACCAGTCCCAGGACACAGTGCTGATATCACAGGAAGA[C/T]
AGATTATCACAGCAACAGAGGTCTCTTTATTATAGAGTAGATGTACAGTCATGTTGGGCTGCGGACAGATCCCGATCTCACAACTGCATTACAAAAGGGA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	40.50%	1.50%	8.89%	49.13%	NA
All Indica	2759	14.90%	0.00%	11.09%	74.01%	NA
All Japonica	1512	90.10%	4.50%	4.10%	1.32%	NA
Aus	269	2.20%	0.00%	16.36%	81.41%	NA
Indica I	595	13.80%	0.00%	6.22%	80.00%	NA
Indica II	465	10.10%	0.00%	6.24%	83.66%	NA
Indica III	913	18.60%	0.00%	17.96%	63.42%	NA
Indica Intermediate	786	14.20%	0.00%	9.67%	76.08%	NA
Temperate Japonica	767	86.40%	7.30%	6.13%	0.13%	NA
Tropical Japonica	504	94.00%	0.60%	1.79%	3.57%	NA
Japonica Intermediate	241	93.40%	3.70%	2.49%	0.41%	NA
VI/Aromatic	96	91.70%	0.00%	3.12%	5.21%	NA
Intermediate	90	53.30%	1.10%	5.56%	40.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0334406362	G -> A	LOC_Os03g60524.1	upstream_gene_variant ; 743.0bp to feature; MODIFIER	silent_mutation	Average:66.919; most accessible tissue: Zhenshan97 flower, score: 89.027	N	N	N	N
vg0334406362	G -> A	LOC_Os03g60530.1	upstream_gene_variant ; 731.0bp to feature; MODIFIER	silent_mutation	Average:66.919; most accessible tissue: Zhenshan97 flower, score: 89.027	N	N	N	N
vg0334406362	G -> A	LOC_Os03g60530.3	upstream_gene_variant ; 731.0bp to feature; MODIFIER	silent_mutation	Average:66.919; most accessible tissue: Zhenshan97 flower, score: 89.027	N	N	N	N
vg0334406362	G -> A	LOC_Os03g60540.1	downstream_gene_variant ; 4500.0bp to feature; MODIFIER	silent_mutation	Average:66.919; most accessible tissue: Zhenshan97 flower, score: 89.027	N	N	N	N
vg0334406362	G -> A	LOC_Os03g60524-LOC_Os03g60530	intergenic_region ; MODIFIER	silent_mutation	Average:66.919; most accessible tissue: Zhenshan97 flower, score: 89.027	N	N	N	N
vg0334406362	G -> DEL	N	N	silent_mutation	Average:66.919; most accessible tissue: Zhenshan97 flower, score: 89.027	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0334406362	3.00E-06	NA	mr1627	Jap_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