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Detailed information for vg0232031755:

Variant ID: vg0232031755 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 32031755
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATGATCAATCAAGTGCCACACTAGCTCTACAAATGGAAGCGATGCACTTGACTCTTGGCTAATCAACCCTCTAACACACTAGATAGATGAACACAAAGCT[C/T]
AAGTGGGTGTGAGAGAGGTGCAAGGGATGTATGCAATTGAATTGGGTGCCAAGAGAGTCCCCTTGTTGCTGGTGGGGAAGTATTTATACTCCCACCCACC

Reverse complement sequence

GGTGGGTGGGAGTATAAATACTTCCCCACCAGCAACAAGGGGACTCTCTTGGCACCCAATTCAATTGCATACATCCCTTGCACCTCTCTCACACCCACTT[G/A]
AGCTTTGTGTTCATCTATCTAGTGTGTTAGAGGGTTGATTAGCCAAGAGTCAAGTGCATCGCTTCCATTTGTAGAGCTAGTGTGGCACTTGATTGATCAT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	92.00%	0.20%	3.13%	4.59%	NA
All Indica	2759	86.50%	0.40%	5.26%	7.83%	NA
All Japonica	1512	99.90%	0.00%	0.07%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	80.50%	0.20%	7.56%	11.76%	NA
Indica II	465	87.70%	0.60%	4.95%	6.67%	NA
Indica III	913	87.60%	0.70%	4.16%	7.56%	NA
Indica Intermediate	786	89.10%	0.10%	4.96%	5.85%	NA
Temperate Japonica	767	99.90%	0.00%	0.13%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	96.70%	0.00%	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
vg0232031755	C -> T	LOC_Os02g52314.1	upstream_gene_variant ; 4603.0bp to feature; MODIFIER	silent_mutation	Average:24.178; most accessible tissue: Minghui63 panicle, score: 34.226	N	N	N	N
vg0232031755	C -> T	LOC_Os02g52330.1	intron_variant ; MODIFIER	silent_mutation	Average:24.178; most accessible tissue: Minghui63 panicle, score: 34.226	N	N	N	N
vg0232031755	C -> DEL	N	N	silent_mutation	Average:24.178; most accessible tissue: Minghui63 panicle, score: 34.226	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0232031755	3.58E-06	NA	mr1531_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