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Detailed information for vg0623976109:

Variant ID: vg0623976109 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 23976109
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CGGTTGCGAGTTGTTGAGCTTCCTCGACGCTTACTCCGGTTACCACCAAATAAGCATGGCAAAAGAGGACGAGGATAAGACAGCATTCATCACGCCGTTC[G/A]
GGGTATTCTGCTACGTTAAGATGCCATTCGGACTAATAACCACAGGAAACACTTTCCAGCGCACGGTCCAAGGTGCACTTAGTGACCAGCTCGGAAACAA

Reverse complement sequence

TTGTTTCCGAGCTGGTCACTAAGTGCACCTTGGACCGTGCGCTGGAAAGTGTTTCCTGTGGTTATTAGTCCGAATGGCATCTTAACGTAGCAGAATACCC[C/T]
GAACGGCGTGATGAATGCTGTCTTATCCTCGTCCTCTTTTGCCATGCTTATTTGGTGGTAACCGGAGTAAGCGTCGAGGAAGCTCAACAACTCGCAACCG

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	51.80%	22.20%	9.33%	16.67%	NA
All Indica	2759	24.30%	36.50%	15.44%	23.81%	NA
All Japonica	1512	90.20%	0.80%	0.40%	8.60%	NA
Aus	269	96.30%	3.70%	0.00%	0.00%	NA
Indica I	595	4.90%	38.70%	30.59%	25.88%	NA
Indica II	465	22.60%	48.40%	9.89%	19.14%	NA
Indica III	913	35.50%	27.20%	9.97%	27.38%	NA
Indica Intermediate	786	27.00%	38.50%	13.61%	20.87%	NA
Temperate Japonica	767	96.90%	1.00%	0.13%	1.96%	NA
Tropical Japonica	504	78.60%	0.40%	0.99%	20.04%	NA
Japonica Intermediate	241	93.40%	0.80%	0.00%	5.81%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	64.40%	24.40%	10.00%	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
vg0623976109	G -> A	LOC_Os06g40240.1	missense_variant ; p.Gly1645Arg; MODERATE	nonsynonymous_codon ; G1645K	Average:51.697; most accessible tissue: Minghui63 flag leaf, score: 82.75	probably damaging	2.124	DELETERIOUS	0.00
vg0623976109	G -> A	LOC_Os06g40240.1	missense_variant ; p.Gly1645Arg; MODERATE	nonsynonymous_codon ; G1645R	Average:51.697; most accessible tissue: Minghui63 flag leaf, score: 82.75	probably damaging	2.375	DELETERIOUS	0.03
vg0623976109	G -> DEL	LOC_Os06g40240.1	N	frameshift_variant	Average:51.697; most accessible tissue: Minghui63 flag leaf, score: 82.75	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0623976109	2.95E-06	NA	mr1896	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