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Detailed information for vg0608855554:

Variant ID: vg0608855554 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 8855554
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AACATCTGCTCGGCATTCGCCAAAGGCCGGGAGAGTCGATAAGAGAATACATGCGTCGCTTCTCGCAAGCCTGGTGCCAAGTTCAAGACATAACCGAGGC[A/G]
TCAGTCATAAATGCTGCTTCGGCTGGTCTGCTTGTCACGCCCGGAAATTCACTAGTAATTTCCGAACTTATTTGTGCATAAAATCCTCGTCCAGGAATCA

Reverse complement sequence

TGATTCCTGGACGAGGATTTTATGCACAAATAAGTTCGGAAATTACTAGTGAATTTCCGGGCGTGACAAGCAGACCAGCCGAAGCAGCATTTATGACTGA[T/C]
GCCTCGGTTATGTCTTGAACTTGGCACCAGGCTTGCGAGAAGCGACGCATGTATTCTCTTATCGACTCTCCCGGCCTTTGGCGAATGCCGAGCAGATGTT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	15.20%	0.20%	56.01%	28.57%	NA
All Indica	2759	4.30%	0.30%	87.71%	7.72%	NA
All Japonica	1512	38.40%	0.10%	1.92%	59.59%	NA
Aus	269	2.60%	0.00%	53.53%	43.87%	NA
Indica I	595	4.90%	0.00%	81.18%	13.95%	NA
Indica II	465	5.20%	0.20%	88.17%	6.45%	NA
Indica III	913	3.80%	0.40%	92.44%	3.29%	NA
Indica Intermediate	786	3.90%	0.30%	86.90%	8.91%	NA
Temperate Japonica	767	71.30%	0.00%	0.91%	27.77%	NA
Tropical Japonica	504	2.60%	0.40%	2.38%	94.64%	NA
Japonica Intermediate	241	8.30%	0.00%	4.15%	87.55%	NA
VI/Aromatic	96	1.00%	0.00%	9.38%	89.58%	NA
Intermediate	90	14.40%	0.00%	50.00%	35.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0608855554	A -> G	LOC_Os06g15630.1	synonymous_variant ; p.Ala493Ala; LOW	synonymous_codon	Average:16.991; most accessible tissue: Minghui63 panicle, score: 25.313	N	N	N	N
vg0608855554	A -> DEL	LOC_Os06g15630.1	N	frameshift_variant	Average:16.991; most accessible tissue: Minghui63 panicle, score: 25.313	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0608855554	NA	9.28E-07	mr1428_2	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