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Detailed information for vg0711014575:

Variant ID: vg0711014575 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 11014575
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TACTCCAAGATATATAATCGTGGTGTCGTCTTGAATCACACATGATCTATATCCAATTTTGTTATTAGTCCGACAACCTCTTCTTGTACCACGACCTTCC[G/A]
TTGTCCCATTTGTAATTCTCTCTGAGTTGAGTTTTAGAAGTCCTACTATCATTTTCTATCCAATATTTCGTGGAGGAAAAGGTCCAACCCACCCTAAACT

Reverse complement sequence

AGTTTAGGGTGGGTTGGACCTTTTCCTCCACGAAATATTGGATAGAAAATGATAGTAGGACTTCTAAAACTCAACTCAGAGAGAATTACAAATGGGACAA[C/T]
GGAAGGTCGTGGTACAAGAAGAGGTTGTCGGACTAATAACAAAATTGGATATAGATCATGTGTGATTCAAGACGACACCACGATTATATATCTTGGAGTA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	98.00%	1.70%	0.02%	0.25%	NA
All Indica	2759	100.00%	0.00%	0.00%	0.00%	NA
All Japonica	1512	94.80%	4.40%	0.00%	0.79%	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	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.90%	0.10%	0.00%	0.00%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	84.90%	12.70%	0.00%	2.38%	NA
Japonica Intermediate	241	99.20%	0.80%	0.00%	0.00%	NA
VI/Aromatic	96	93.80%	6.20%	0.00%	0.00%	NA
Intermediate	90	91.10%	7.80%	1.11%	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
vg0711014575	G -> DEL	N	N	silent_mutation	Average:30.796; most accessible tissue: Callus, score: 62.311	N	N	N	N
vg0711014575	G -> A	LOC_Os07g18630-LOC_Os07g18640	intergenic_region ; MODIFIER	silent_mutation	Average:30.796; most accessible tissue: Callus, score: 62.311	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0711014575	5.26E-07	5.26E-07	mr1389	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