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Detailed information for vg0622627470:

Variant ID: vg0622627470 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 22627470
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGAAGCAGGACTTCGAAGCAATGATGCAACAAGCACGGGATCAGTATCTGAGCTCATACATGCAAACCCGCAAGGGATCACTCGTTCAGAAGTACAAGTT[G/A]
AAGCTAGTCGCCGACATCCCTGGAACCGGTTCATCTAAAGATGGGGAAATTAAGCGAGATCCAGATGGCTCGGCTCAGCCGAGCGCCAAAGGAGCTACCG

Reverse complement sequence

CGGTAGCTCCTTTGGCGCTCGGCTGAGCCGAGCCATCTGGATCTCGCTTAATTTCCCCATCTTTAGATGAACCGGTTCCAGGGATGTCGGCGACTAGCTT[C/T]
AACTTGTACTTCTGAACGAGTGATCCCTTGCGGGTTTGCATGTATGAGCTCAGATACTGATCCCGTGCTTGTTGCATCATTGCTTCGAAGTCCTGCTTCT

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	92.30%	4.30%	2.96%	0.42%	NA
All Indica	2759	97.70%	1.00%	1.30%	0.00%	NA
All Japonica	1512	81.10%	11.40%	6.28%	1.26%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.80%	0.00%	0.17%	0.00%	NA
Indica II	465	99.40%	0.40%	0.22%	0.00%	NA
Indica III	913	94.90%	2.10%	3.07%	0.00%	NA
Indica Intermediate	786	98.30%	0.90%	0.76%	0.00%	NA
Temperate Japonica	767	82.80%	8.20%	7.17%	1.83%	NA
Tropical Japonica	504	77.80%	17.70%	4.17%	0.40%	NA
Japonica Intermediate	241	82.60%	8.30%	7.88%	1.24%	NA
VI/Aromatic	96	91.70%	1.00%	7.29%	0.00%	NA
Intermediate	90	93.30%	3.30%	2.22%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0622627470	G -> A	LOC_Os06g38240.1	synonymous_variant ; p.Leu27Leu; LOW	synonymous_codon	Average:52.086; most accessible tissue: Zhenshan97 flag leaf, score: 78.512	N	N	N	N
vg0622627470	G -> DEL	LOC_Os06g38240.1	N	frameshift_variant	Average:52.086; most accessible tissue: Zhenshan97 flag leaf, score: 78.512	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0622627470	2.78E-06	1.30E-06	mr1078_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