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Detailed information for vg0406706405:

Variant ID: vg0406706405 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 6706405
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TATTGACACAGAACTCAATAGCCTCCTCGGTCGTGTAACCTTCAATGATGCTCCCCTCGGGTTTAGCTCTGTTACAAACGTACGACTTCAGAACTCCCAT[G/A]
TACCTTTCAAACGGCCACATTTCCCTTTGAAAAGCCGGGCCACATAGTTTTGTTTGCTTCACCAGATGAACAGGGAGATGAACCATTATATCAAAAAAAG

Reverse complement sequence

CTTTTTTTGATATAATGGTTCATCTCCCTGTTCATCTGGTGAAGCAAACAAAACTATGTGGCCCGGCTTTTCAAAGGGAAATGTGGCCGTTTGAAAGGTA[C/T]
ATGGGAGTTCTGAAGTCGTACGTTTGTAACAGAGCTAAACCCGAGGGGAGCATCATTGAAGGTTACACGACCGAGGAGGCTATTGAGTTCTGTGTCAATA

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	87.50%	0.30%	2.50%	9.71%	NA
All Indica	2759	87.70%	0.40%	2.90%	9.03%	NA
All Japonica	1512	98.90%	0.00%	0.60%	0.53%	NA
Aus	269	27.10%	0.70%	9.29%	62.83%	NA
Indica I	595	97.30%	0.20%	0.34%	2.18%	NA
Indica II	465	79.80%	0.40%	4.73%	15.05%	NA
Indica III	913	87.00%	0.50%	3.29%	9.20%	NA
Indica Intermediate	786	85.90%	0.40%	3.31%	10.43%	NA
Temperate Japonica	767	99.50%	0.00%	0.26%	0.26%	NA
Tropical Japonica	504	99.00%	0.00%	0.40%	0.60%	NA
Japonica Intermediate	241	96.70%	0.00%	2.07%	1.24%	NA
VI/Aromatic	96	70.80%	0.00%	4.17%	25.00%	NA
Intermediate	90	90.00%	0.00%	0.00%	10.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0406706405	G -> DEL	LOC_Os04g12170.1	N	frameshift_variant	Average:15.933; most accessible tissue: Minghui63 flag leaf, score: 32.882	N	N	N	N
vg0406706405	G -> A	LOC_Os04g12170.1	synonymous_variant ; p.Tyr423Tyr; LOW	synonymous_codon	Average:15.933; most accessible tissue: Minghui63 flag leaf, score: 32.882	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0406706405	5.29E-07	NA	mr1865_2	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