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Detailed information for vg0212300877:

Variant ID: vg0212300877 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 12300877
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGGGGTACGCTGGTACGAGGATCTACATAATACGACATCAAGCAGGCAGAAAACAAAGATTATACTGGTTTAGGCCCCTTGATAGGTAATAGCCCTAATC[C/T]
AGTTGATATGGGATTATATGATGGAAACCACATATTACAAAGGGAATAGCGGAACTCGACGATACCGACGAGATCGTAGTCGAATTGATTCGACTAGATC

Reverse complement sequence

GATCTAGTCGAATCAATTCGACTACGATCTCGTCGGTATCGTCGAGTTCCGCTATTCCCTTTGTAATATGTGGTTTCCATCATATAATCCCATATCAACT[G/A]
GATTAGGGCTATTACCTATCAAGGGGCCTAAACCAGTATAATCTTTGTTTTCTGCCTGCTTGATGTCGTATTATGTAGATCCTCGTACCAGCGTACCCCA

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	72.70%	0.20%	2.39%	24.76%	NA
All Indica	2759	56.50%	0.30%	3.84%	39.36%	NA
All Japonica	1512	99.00%	0.00%	0.00%	0.99%	NA
Aus	269	78.80%	0.00%	2.23%	18.96%	NA
Indica I	595	55.00%	0.00%	6.39%	38.66%	NA
Indica II	465	57.00%	0.60%	3.44%	38.92%	NA
Indica III	913	50.70%	0.70%	2.52%	46.11%	NA
Indica Intermediate	786	64.00%	0.00%	3.69%	32.32%	NA
Temperate Japonica	767	99.50%	0.00%	0.00%	0.52%	NA
Tropical Japonica	504	98.20%	0.00%	0.00%	1.79%	NA
Japonica Intermediate	241	99.20%	0.00%	0.00%	0.83%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	78.90%	0.00%	1.11%	20.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0212300877	C -> T	LOC_Os02g20820.1	downstream_gene_variant ; 4961.0bp to feature; MODIFIER	silent_mutation	Average:21.402; most accessible tissue: Minghui63 panicle, score: 50.413	N	N	N	N
vg0212300877	C -> T	LOC_Os02g20810-LOC_Os02g20820	intergenic_region ; MODIFIER	silent_mutation	Average:21.402; most accessible tissue: Minghui63 panicle, score: 50.413	N	N	N	N
vg0212300877	C -> DEL	N	N	silent_mutation	Average:21.402; most accessible tissue: Minghui63 panicle, score: 50.413	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0212300877	2.88E-07	7.07E-09	mr1004	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
vg0212300877	1.50E-07	4.70E-08	mr1005	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
vg0212300877	5.19E-09	9.39E-08	mr1011	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
vg0212300877	7.30E-08	2.11E-07	mr1012	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