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Detailed information for vg0711196957:

Variant ID: vg0711196957 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 11196957
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.94, A: 0.09, others allele: 0.00, population size: 32. )

Flanking Sequence (100 bp) in Reference Genome:

TTGAACTCACTTCCACTCAAGGCGCTAAGAATTGCATTAGCGGCTTGAGCGTTCTTGTGCTCGTTCTCGTCGTCCTCCTTGGTGGGTTCCTCGGGATTCT[G/A]
CAAAACATAGCCTTTTTCGACTATTCTCCAAATCAAAGGGTTAATAGATTTCAAATGCATCTTCATCTTATGTTTCCAAGCGGCATAGTCCGTACCATTG

Reverse complement sequence

CAATGGTACGGACTATGCCGCTTGGAAACATAAGATGAAGATGCATTTGAAATCTATTAACCCTTTGATTTGGAGAATAGTCGAAAAAGGCTATGTTTTG[C/T]
AGAATCCCGAGGAACCCACCAAGGAGGACGACGAGAACGAGCACAAGAACGCTCAAGCCGCTAATGCAATTCTTAGCGCCTTGAGTGGAAGTGAGTTCAA

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	36.50%	5.60%	24.40%	33.47%	NA
All Indica	2759	7.60%	9.20%	37.37%	45.78%	NA
All Japonica	1512	85.60%	0.40%	1.79%	12.24%	NA
Aus	269	26.00%	1.10%	28.25%	44.61%	NA
Indica I	595	8.60%	12.80%	41.18%	37.48%	NA
Indica II	465	7.10%	8.00%	34.62%	50.32%	NA
Indica III	913	4.20%	7.40%	33.52%	54.87%	NA
Indica Intermediate	786	11.30%	9.30%	40.59%	38.80%	NA
Temperate Japonica	767	74.60%	0.70%	2.61%	22.16%	NA
Tropical Japonica	504	99.60%	0.00%	0.20%	0.20%	NA
Japonica Intermediate	241	91.30%	0.40%	2.49%	5.81%	NA
VI/Aromatic	96	95.80%	1.00%	1.04%	2.08%	NA
Intermediate	90	64.40%	2.20%	20.00%	13.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0711196957	G -> DEL	LOC_Os07g18890.1	N	frameshift_variant	Average:9.056; most accessible tissue: Callus, score: 43.983	N	N	N	N
vg0711196957	G -> A	LOC_Os07g18890.1	stop_gained ; p.Gln73*; HIGH	stop_gained	Average:9.056; most accessible tissue: Callus, score: 43.983	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0711196957	2.61E-06	9.65E-06	mr1497_2	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