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Detailed information for vg0721197653:

Variant ID: vg0721197653 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 21197653
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 107. )

Flanking Sequence (100 bp) in Reference Genome:

GTATGTCAAGTGGGATAAATTGGTTCTCTTGGGAAGCATAACTTATAGTTAGAGTGGTCGACCCTTGCATCGAATAGCTGAAGTACCTAGCACCGGAGAC[C/T]
AGGAAAGCTAATATGAGACAGTTGATGGCAAGTTAGAAGTGAATGACAAGCATGATATTCTTATGATGACAAACATAGTATCCTAGTAATGACAAGCTAG

Reverse complement sequence

CTAGCTTGTCATTACTAGGATACTATGTTTGTCATCATAAGAATATCATGCTTGTCATTCACTTCTAACTTGCCATCAACTGTCTCATATTAGCTTTCCT[G/A]
GTCTCCGGTGCTAGGTACTTCAGCTATTCGATGCAAGGGTCGACCACTCTAACTATAAGTTATGCTTCCCAAGAGAACCAATTTATCCCACTTGACATAC

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	30.40%	9.70%	5.73%	54.15%	NA
All Indica	2759	8.50%	9.00%	6.20%	76.33%	NA
All Japonica	1512	71.40%	0.10%	2.18%	26.32%	NA
Aus	269	17.10%	72.50%	7.06%	3.35%	NA
Indica I	595	9.20%	2.70%	2.35%	85.71%	NA
Indica II	465	9.20%	6.90%	4.73%	79.14%	NA
Indica III	913	4.30%	10.30%	9.53%	75.90%	NA
Indica Intermediate	786	12.50%	13.40%	6.11%	68.07%	NA
Temperate Japonica	767	82.40%	0.00%	0.91%	16.69%	NA
Tropical Japonica	504	52.00%	0.20%	3.17%	44.64%	NA
Japonica Intermediate	241	76.80%	0.40%	4.15%	18.67%	NA
VI/Aromatic	96	39.60%	4.20%	42.71%	13.54%	NA
Intermediate	90	43.30%	12.20%	7.78%	36.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0721197653	C -> DEL	N	N	silent_mutation	Average:5.621; most accessible tissue: Callus, score: 9.624	N	N	N	N
vg0721197653	C -> T	LOC_Os07g35450.1	upstream_gene_variant ; 2893.0bp to feature; MODIFIER	silent_mutation	Average:5.621; most accessible tissue: Callus, score: 9.624	N	N	N	N
vg0721197653	C -> T	LOC_Os07g35440.1	intron_variant ; MODIFIER	silent_mutation	Average:5.621; most accessible tissue: Callus, score: 9.624	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0721197653	6.79E-07	1.23E-13	mr1216	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
vg0721197653	1.07E-08	1.30E-15	mr1216	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
vg0721197653	NA	6.19E-06	mr1158_2	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
vg0721197653	NA	9.78E-06	mr1952_2	Ind_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