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Detailed information for vg0712641466:

Variant ID: vg0712641466 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 12641466
Reference Allele: G	Alternative Allele: C
Primary Allele: G	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GGAAACCACCCGTTCCTTTGTCACCTCCCGATCCTATGGAACTCGGGTTCCTGTGAGAAACTGTCCGAGTTGACATCCATAATGAGCAATGAATGGCTAA[G/C]
GGAGGTAGAGCTTTCATCCGAAGTAATTCAGATAAATACGGCTCCCCGAATCATTCCATGCCATCTAGAAGGGAACGATGTCGGTATTCTCTACAGTCCA

Reverse complement sequence

TGGACTGTAGAGAATACCGACATCGTTCCCTTCTAGATGGCATGGAATGATTCGGGGAGCCGTATTTATCTGAATTACTTCGGATGAAAGCTCTACCTCC[C/G]
TTAGCCATTCATTGCTCATTATGGATGTCAACTCGGACAGTTTCTCACAGGAACCCGAGTTCCATAGGATCGGGAGGTGACAAAGGAACGGGTGGTTTCC

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	82.60%	0.10%	2.09%	15.19%	NA
All Indica	2759	75.30%	0.30%	3.48%	20.95%	NA
All Japonica	1512	98.90%	0.00%	0.00%	1.06%	NA
Aus	269	62.10%	0.00%	0.37%	37.55%	NA
Indica I	595	63.00%	0.20%	4.71%	32.10%	NA
Indica II	465	78.10%	0.00%	2.80%	19.14%	NA
Indica III	913	78.00%	0.50%	3.94%	17.52%	NA
Indica Intermediate	786	79.90%	0.10%	2.42%	17.56%	NA
Temperate Japonica	767	99.10%	0.00%	0.00%	0.91%	NA
Tropical Japonica	504	99.40%	0.00%	0.00%	0.60%	NA
Japonica Intermediate	241	97.50%	0.00%	0.00%	2.49%	NA
VI/Aromatic	96	90.60%	0.00%	1.04%	8.33%	NA
Intermediate	90	82.20%	0.00%	1.11%	16.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0712641466	G -> DEL	LOC_Os07g22480.1	N	frameshift_variant	Average:10.963; most accessible tissue: Callus, score: 28.528	N	N	N	N
vg0712641466	G -> C	LOC_Os07g22480.1	missense_variant ; p.Arg7Thr; MODERATE	nonsynonymous_codon ; R7T	Average:10.963; most accessible tissue: Callus, score: 28.528	possibly damaging	1.521	DELETERIOUS	0.00

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0712641466	NA	2.09E-06	mr1197	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
vg0712641466	2.86E-06	NA	mr1877	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