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Detailed information for vg0711096071:

Variant ID: vg0711096071 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 11096071
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GCAATATGTTAGCGTGCAGGTGGAGCACGTGGATGATCAGGAAACTGAAATTGTTGGTAATGATGTTAATGATATTATTCAGCACTCACCTCTTGTTTTG[C/T]
AGCCACAAGATGAACCTATTGCACATCGCAGAACAAAGAGGAGTTGTGGAGCTCCAGTCTGCCTTATTGAGGAATGTGATATGGTTTATTATGCTTTTAG

Reverse complement sequence

CTAAAAGCATAATAAACCATATCACATTCCTCAATAAGGCAGACTGGAGCTCCACAACTCCTCTTTGTTCTGCGATGTGCAATAGGTTCATCTTGTGGCT[G/A]
CAAAACAAGAGGTGAGTGCTGAATAATATCATTAACATCATTACCAACAATTTCAGTTTCCTGATCATCCACGTGCTCCACCTGCACGCTAACATATTGC

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	36.20%	5.60%	46.32%	11.87%	NA
All Indica	2759	12.60%	8.30%	72.92%	6.13%	NA
All Japonica	1512	74.90%	0.90%	2.25%	22.02%	NA
Aus	269	63.60%	4.80%	26.02%	5.58%	NA
Indica I	595	7.10%	4.00%	85.88%	3.03%	NA
Indica II	465	16.10%	4.70%	75.05%	4.09%	NA
Indica III	913	12.80%	13.90%	67.03%	6.24%	NA
Indica Intermediate	786	14.50%	7.30%	68.70%	9.54%	NA
Temperate Japonica	767	65.40%	0.10%	2.09%	32.33%	NA
Tropical Japonica	504	86.10%	2.00%	2.38%	9.52%	NA
Japonica Intermediate	241	81.30%	0.80%	2.49%	15.35%	NA
VI/Aromatic	96	17.70%	4.20%	40.62%	37.50%	NA
Intermediate	90	48.90%	4.40%	37.78%	8.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0711096071	C -> DEL	LOC_Os07g18760.1	N	frameshift_variant	Average:14.812; most accessible tissue: Minghui63 root, score: 27.443	N	N	N	N
vg0711096071	C -> T	LOC_Os07g18760.1	stop_gained ; p.Gln688*; HIGH	stop_gained	Average:14.812; most accessible tissue: Minghui63 root, score: 27.443	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0711096071	1.82E-06	NA	mr1789	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
vg0711096071	2.58E-06	1.96E-06	mr1789	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