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Detailed information for vg0432880368:

Variant ID: vg0432880368 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 32880368
Reference Allele: C	Alternative Allele: G,T
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTTTCTCAGGGCAGTTCCCGAGCCGGGTTCCCTGGATCCATTCTGACCTAATTGGATGAATGAAGAAGGGGGCGAGCAGATACGACGGCCTCTTTTTAGC[C/G,T]
GAATAAAGCTGGATCTACTACATAGGGAAAGATTAAGAAAGCAAGAGCAAGCCTACTCTACTATCGATTCAAAAGGTAAACTGCCCCCGAAGACTTTATC

Reverse complement sequence

GATAAAGTCTTCGGGGGCAGTTTACCTTTTGAATCGATAGTAGAGTAGGCTTGCTCTTGCTTTCTTAATCTTTCCCTATGTAGTAGATCCAGCTTTATTC[G/C,A]
GCTAAAAAGAGGCCGTCGTATCTGCTCGCCCCCTTCTTCATTCATCCAATTAGGTCAGAATGGATCCAGGGAACCCGGCTCGGGAACTGCCCTGAGAAAA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	92.70%	7.10%	0.19%	0.00%	T: 0.04%
All Indica	2759	99.10%	0.90%	0.04%	0.00%	NA
All Japonica	1512	80.50%	18.80%	0.53%	0.00%	T: 0.13%
Aus	269	98.90%	1.10%	0.00%	0.00%	NA
Indica I	595	97.00%	2.90%	0.17%	0.00%	NA
Indica II	465	99.80%	0.20%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.10%	0.90%	0.00%	0.00%	NA
Temperate Japonica	767	88.00%	11.10%	0.65%	0.00%	T: 0.26%
Tropical Japonica	504	77.40%	22.60%	0.00%	0.00%	NA
Japonica Intermediate	241	63.10%	35.70%	1.24%	0.00%	NA
VI/Aromatic	96	83.30%	16.70%	0.00%	0.00%	NA
Intermediate	90	92.20%	7.80%	0.00%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0432880368	C -> G	LOC_Os04g55300-LOC_Os04g55310	intergenic_region ; MODIFIER	silent_mutation	Average:15.311; most accessible tissue: Callus, score: 24.52	N	N	N	N
vg0432880368	C -> T	LOC_Os04g55300-LOC_Os04g55310	intergenic_region ; MODIFIER	silent_mutation	Average:15.311; most accessible tissue: Callus, score: 24.52	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0432880368	1.75E-06	3.64E-06	mr1150_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