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Detailed information for vg0301373348:

Variant ID: vg0301373348 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 1373348
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CGATCGGATCATGGGCAGAGCTACGCGACCACTTCATCGCCAACTTCCAAGGCACTTTTGAACGGCCTGGTACACACTTCGATCTCTACAACATCATTCA[G/A]
AAGTCTAGAGAGTCTCATCAAGATTACATTCGACGCTTCTCTGAGCAATGCAACAAGATCTCCGACATCACGGACGACGTCATCATTGCCGCCTTTACTA

Reverse complement sequence

TAGTAAAGGCGGCAATGATGACGTCGTCCGTGATGTCGGAGATCTTGTTGCATTGCTCAGAGAAGCGTCGAATGTAATCTTGATGAGACTCTCTAGACTT[C/T]
TGAATGATGTTGTAGAGATCGAAGTGTGTACCAGGCCGTTCAAAAGTGCCTTGGAAGTTGGCGATGAAGTGGTCGCGTAGCTCTGCCCATGATCCGATCG

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	43.90%	0.20%	17.25%	38.57%	NA
All Indica	2759	11.90%	0.30%	26.21%	61.62%	NA
All Japonica	1512	96.00%	0.00%	0.33%	3.64%	NA
Aus	269	72.90%	0.70%	20.45%	5.95%	NA
Indica I	595	16.50%	0.30%	8.40%	74.79%	NA
Indica II	465	13.50%	0.40%	35.27%	50.75%	NA
Indica III	913	5.00%	0.20%	34.06%	60.68%	NA
Indica Intermediate	786	15.30%	0.40%	25.19%	59.16%	NA
Temperate Japonica	767	99.50%	0.00%	0.00%	0.52%	NA
Tropical Japonica	504	90.70%	0.00%	0.40%	8.93%	NA
Japonica Intermediate	241	96.30%	0.00%	1.24%	2.49%	NA
VI/Aromatic	96	51.00%	0.00%	20.83%	28.12%	NA
Intermediate	90	58.90%	0.00%	13.33%	27.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0301373348	G -> A	LOC_Os03g03230.1	synonymous_variant ; p.Gln390Gln; LOW	synonymous_codon	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0301373348	G -> DEL	LOC_Os03g03230.1	N	frameshift_variant	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0301373348	4.04E-06	NA	mr1471	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