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Detailed information for vg0701901151:

Variant ID: vg0701901151 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 1901151
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTGGATACAATATCGTTGCTTTTTGCGATGTAAGTGTGCATTTTTATTGACCAATATTATGGCTTAGGCTGATTATATATTGTGGTCATTTTCCAGGCAG[C/T]
TGGTAAATCCTTTATGAGTTTATTTACTTGGATTTTACACCACATATGCTGTATATTTCTAGGTGTGGTGAAACCATGTGTCTTTTAGGGACTTAAGCAC

Reverse complement sequence

GTGCTTAAGTCCCTAAAAGACACATGGTTTCACCACACCTAGAAATATACAGCATATGTGGTGTAAAATCCAAGTAAATAAACTCATAAAGGATTTACCA[G/A]
CTGCCTGGAAAATGACCACAATATATAATCAGCCTAAGCCATAATATTGGTCAATAAAAATGCACACTTACATCGCAAAAAGCAACGATATTGTATCCAA

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	95.80%	0.30%	1.16%	2.69%	NA
All Indica	2759	98.90%	0.50%	0.22%	0.29%	NA
All Japonica	1512	99.90%	0.00%	0.07%	0.00%	NA
Aus	269	45.40%	0.00%	11.52%	43.12%	NA
Indica I	595	98.70%	0.80%	0.34%	0.17%	NA
Indica II	465	98.90%	0.60%	0.43%	0.00%	NA
Indica III	913	99.80%	0.10%	0.00%	0.11%	NA
Indica Intermediate	786	98.20%	0.80%	0.25%	0.76%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.00%	0.41%	0.00%	NA
VI/Aromatic	96	84.40%	0.00%	13.54%	2.08%	NA
Intermediate	90	94.40%	0.00%	4.44%	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
vg0701901151	C -> DEL	N	N	silent_mutation	Average:26.607; most accessible tissue: Zhenshan97 panicle, score: 39.652	N	N	N	N
vg0701901151	C -> T	LOC_Os07g04290.1	downstream_gene_variant ; 4814.0bp to feature; MODIFIER	silent_mutation	Average:26.607; most accessible tissue: Zhenshan97 panicle, score: 39.652	N	N	N	N
vg0701901151	C -> T	LOC_Os07g04300.1	downstream_gene_variant ; 3195.0bp to feature; MODIFIER	silent_mutation	Average:26.607; most accessible tissue: Zhenshan97 panicle, score: 39.652	N	N	N	N
vg0701901151	C -> T	LOC_Os07g04310.1	downstream_gene_variant ; 1969.0bp to feature; MODIFIER	silent_mutation	Average:26.607; most accessible tissue: Zhenshan97 panicle, score: 39.652	N	N	N	N
vg0701901151	C -> T	LOC_Os07g04300-LOC_Os07g04310	intergenic_region ; MODIFIER	silent_mutation	Average:26.607; most accessible tissue: Zhenshan97 panicle, score: 39.652	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0701901151	6.69E-06	NA	mr1508_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