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Detailed information for vg0622533129:

Variant ID: vg0622533129 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 22533129
Reference Allele: A	Alternative Allele: C
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CAGGCCTCCATCTGTCTACAAGTGCAGAGCATTGAACACTGGCAATCCTCTGTTCACAACCATGGCCACCCCGAGCAACCCAGCTAACGTGAGGTATGGG[A/C]
TGTACCTCTCGTCAAACACCCGGGGGGGTATGCGCTCTAACTCGGAGTGGTTGAAGCACCTATGGAAGCATTTTTAAATCAACCAGTTAGTAAAATGTAA

Reverse complement sequence

TTACATTTTACTAACTGGTTGATTTAAAAATGCTTCCATAGGTGCTTCAACCACTCCGAGTTAGAGCGCATACCCCCCCGGGTGTTTGACGAGAGGTACA[T/G]
CCCATACCTCACGTTAGCTGGGTTGCTCGGGGTGGCCATGGTTGTGAACAGAGGATTGCCAGTGTTCAATGCTCTGCACTTGTAGACAGATGGAGGCCTG

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	92.40%	2.30%	1.71%	3.51%	NA
All Indica	2759	93.80%	0.10%	0.29%	5.84%	NA
All Japonica	1512	88.00%	7.10%	4.70%	0.20%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	92.50%	0.00%	0.22%	7.31%	NA
Indica III	913	89.30%	0.00%	0.44%	10.30%	NA
Indica Intermediate	786	95.20%	0.30%	0.38%	4.20%	NA
Temperate Japonica	767	94.40%	0.70%	4.56%	0.39%	NA
Tropical Japonica	504	77.00%	19.60%	3.37%	0.00%	NA
Japonica Intermediate	241	90.50%	1.70%	7.88%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	94.40%	1.10%	2.22%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0622533129	A -> C	LOC_Os06g38100.1	upstream_gene_variant ; 3471.0bp to feature; MODIFIER	silent_mutation	Average:62.826; most accessible tissue: Zhenshan97 young leaf, score: 86.383	N	N	N	N
vg0622533129	A -> C	LOC_Os06g38090.1	intron_variant ; MODIFIER	silent_mutation	Average:62.826; most accessible tissue: Zhenshan97 young leaf, score: 86.383	N	N	N	N
vg0622533129	A -> DEL	N	N	silent_mutation	Average:62.826; most accessible tissue: Zhenshan97 young leaf, score: 86.383	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0622533129	NA	3.60E-08	mr1746_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