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Detailed information for vg0826610630:

Variant ID: vg0826610630 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 26610630
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATTATAGTAACTTACTTTATCCTTATGCTTATGCCTGAGTGGCCGCAGGTTTCCTCACCCTTCCCGTCTTCCCCTTCTCCGATATAGTCTCCTGGCCACC[C/T]
CTCTAAATCCCGGTGAACCACCCTCCTCATCTTCCCCTAACCCACCCCTAACTTCTAATTAGTAGGTTTTCTGTCATAATTTAGGTTTTGTTAGTAAAGA

Reverse complement sequence

TCTTTACTAACAAAACCTAAATTATGACAGAAAACCTACTAATTAGAAGTTAGGGGTGGGTTAGGGGAAGATGAGGAGGGTGGTTCACCGGGATTTAGAG[G/A]
GGTGGCCAGGAGACTATATCGGAGAAGGGGAAGACGGGAAGGGTGAGGAAACCTGCGGCCACTCAGGCATAAGCATAAGGATAAAGTAAGTTACTATAAT

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	44.40%	28.90%	10.69%	16.10%	NA
All Indica	2759	18.40%	48.60%	15.37%	17.54%	NA
All Japonica	1512	82.30%	0.40%	1.39%	15.94%	NA
Aus	269	75.80%	0.70%	17.10%	6.32%	NA
Indica I	595	26.40%	40.70%	18.15%	14.79%	NA
Indica II	465	2.60%	79.60%	9.03%	8.82%	NA
Indica III	913	24.40%	30.80%	18.18%	26.62%	NA
Indica Intermediate	786	14.90%	57.10%	13.74%	14.25%	NA
Temperate Japonica	767	95.00%	0.40%	0.26%	4.30%	NA
Tropical Japonica	504	72.00%	0.60%	2.18%	25.20%	NA
Japonica Intermediate	241	63.10%	0.00%	3.32%	33.61%	NA
VI/Aromatic	96	97.90%	0.00%	2.08%	0.00%	NA
Intermediate	90	50.00%	15.60%	13.33%	21.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0826610630	C -> T	LOC_Os08g42110.1	downstream_gene_variant ; 1092.0bp to feature; MODIFIER	silent_mutation	Average:29.501; most accessible tissue: Minghui63 panicle, score: 50.413	N	N	N	N
vg0826610630	C -> T	LOC_Os08g42120.1	downstream_gene_variant ; 2660.0bp to feature; MODIFIER	silent_mutation	Average:29.501; most accessible tissue: Minghui63 panicle, score: 50.413	N	N	N	N
vg0826610630	C -> T	LOC_Os08g42110-LOC_Os08g42120	intergenic_region ; MODIFIER	silent_mutation	Average:29.501; most accessible tissue: Minghui63 panicle, score: 50.413	N	N	N	N
vg0826610630	C -> DEL	N	N	silent_mutation	Average:29.501; 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
vg0826610630	NA	3.50E-09	mr1352	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0826610630	2.62E-06	NA	mr1798_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