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Detailed information for vg0707899397:

Variant ID: vg0707899397 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 7899397
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCTTTGTTCTATTTCTTGTTAATTACAAGATCAAATCAACTGGCACGCTCATACATCCGAAGGTGAGTTTTGGACCTGCACTGGAGTTAAGCAGATCTCC[C/T]
AGGCCTCGTGTTTTCTGTCAAGAACTAGCTCTCAATGACTTGGCTCCTCGCAGATTCCTGCTTCTTAGGCTATGTTGGTTGTATGATTCGATGATCTATG

Reverse complement sequence

CATAGATCATCGAATCATACAACCAACATAGCCTAAGAAGCAGGAATCTGCGAGGAGCCAAGTCATTGAGAGCTAGTTCTTGACAGAAAACACGAGGCCT[G/A]
GGAGATCTGCTTAACTCCAGTGCAGGTCCAAAACTCACCTTCGGATGTATGAGCGTGCCAGTTGATTTGATCTTGTAATTAACAAGAAATAGAACAAAGA

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	96.20%	3.80%	0.02%	0.00%	NA
All Indica	2759	99.60%	0.40%	0.00%	0.00%	NA
All Japonica	1512	90.10%	9.80%	0.07%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	99.00%	1.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.90%	0.10%	0.00%	0.00%	NA
Temperate Japonica	767	84.20%	15.60%	0.13%	0.00%	NA
Tropical Japonica	504	97.80%	2.20%	0.00%	0.00%	NA
Japonica Intermediate	241	92.90%	7.10%	0.00%	0.00%	NA
VI/Aromatic	96	78.10%	21.90%	0.00%	0.00%	NA
Intermediate	90	98.90%	1.10%	0.00%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0707899397	C -> T	LOC_Os07g13760.1	upstream_gene_variant ; 2195.0bp to feature; MODIFIER	silent_mutation	Average:57.658; most accessible tissue: Minghui63 flag leaf, score: 73.334	N	N	N	N
vg0707899397	C -> T	LOC_Os07g13770.1	upstream_gene_variant ; 1176.0bp to feature; MODIFIER	silent_mutation	Average:57.658; most accessible tissue: Minghui63 flag leaf, score: 73.334	N	N	N	N
vg0707899397	C -> T	LOC_Os07g13780.1	upstream_gene_variant ; 4387.0bp to feature; MODIFIER	silent_mutation	Average:57.658; most accessible tissue: Minghui63 flag leaf, score: 73.334	N	N	N	N
vg0707899397	C -> T	LOC_Os07g13760-LOC_Os07g13770	intergenic_region ; MODIFIER	silent_mutation	Average:57.658; most accessible tissue: Minghui63 flag leaf, score: 73.334	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0707899397	2.94E-06	2.94E-06	mr1141_2	Jap_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