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Detailed information for vg0711901487:

Variant ID: vg0711901487 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 11901487
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CTGGGGGCTAGGAAGGGTACCAAACTCCGTTTGCTGAGGGCAACTCTAGCGAACGTACTCTTTTATTGTGACACACAGATTCAACTTATTTTCAATTTTT[C/T]
CATACATATTATAACATGTTACCCTTTAAGCATTCGCTCGGGGGCTATTTCTATTTAATATTATGTTCTGAATAATGATTTCAGGAAAGTTCCATTCAGC

Reverse complement sequence

GCTGAATGGAACTTTCCTGAAATCATTATTCAGAACATAATATTAAATAGAAATAGCCCCCGAGCGAATGCTTAAAGGGTAACATGTTATAATATGTATG[G/A]
AAAAATTGAAAATAAGTTGAATCTGTGTGTCACAATAAAAGAGTACGTTCGCTAGAGTTGCCCTCAGCAAACGGAGTTTGGTACCCTTCCTAGCCCCCAG

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	92.30%	4.30%	0.76%	2.62%	NA
All Indica	2759	98.90%	0.20%	0.62%	0.22%	NA
All Japonica	1512	83.90%	7.10%	1.26%	7.74%	NA
Aus	269	95.20%	4.80%	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	99.90%	0.10%	0.00%	0.00%	NA
Indica Intermediate	786	96.40%	0.60%	2.16%	0.76%	NA
Temperate Japonica	767	73.30%	13.20%	2.09%	11.47%	NA
Tropical Japonica	504	99.40%	0.40%	0.20%	0.00%	NA
Japonica Intermediate	241	85.10%	2.10%	0.83%	12.03%	NA
VI/Aromatic	96	24.00%	75.00%	0.00%	1.04%	NA
Intermediate	90	95.60%	4.40%	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
vg0711901487	C -> DEL	N	N	silent_mutation	Average:48.482; most accessible tissue: Minghui63 flag leaf, score: 69.182	N	N	N	N
vg0711901487	C -> T	LOC_Os07g20590.1	upstream_gene_variant ; 1966.0bp to feature; MODIFIER	silent_mutation	Average:48.482; most accessible tissue: Minghui63 flag leaf, score: 69.182	N	N	N	N
vg0711901487	C -> T	LOC_Os07g20580-LOC_Os07g20590	intergenic_region ; MODIFIER	silent_mutation	Average:48.482; most accessible tissue: Minghui63 flag leaf, score: 69.182	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0711901487	2.95E-06	NA	mr1062_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
vg0711901487	4.02E-06	4.21E-09	mr1062_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