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Detailed information for vg0716100091:

Variant ID: vg0716100091 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 16100091
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 109. )

Flanking Sequence (100 bp) in Reference Genome:

GCGGAGGAGCCCGCGACTACGCCACCTTCCGGGATGCTAGCTCGGAGGATGACGCTACCATCATGCACCTGGCGCGCATGGTGGAGGCGTACGACGCGGC[C/T]
CATATCGACTTCCATCAGATGGTGCGTCGTGGGTTGGTCGAGAACAACATGAAGATCCTGGAGCTGCGTCAGGAGAATCTGCAGCTGAAGAAGGACCTAG

Reverse complement sequence

CTAGGTCCTTCTTCAGCTGCAGATTCTCCTGACGCAGCTCCAGGATCTTCATGTTGTTCTCGACCAACCCACGACGCACCATCTGATGGAAGTCGATATG[G/A]
GCCGCGTCGTACGCCTCCACCATGCGCGCCAGGTGCATGATGGTAGCGTCATCCTCCGAGCTAGCATCCCGGAAGGTGGCGTAGTCGCGGGCTCCTCCGC

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	48.30%	41.60%	9.94%	0.13%	NA
All Indica	2759	76.50%	10.50%	12.94%	0.00%	NA
All Japonica	1512	0.50%	99.10%	0.13%	0.26%	NA
Aus	269	48.30%	16.00%	35.69%	0.00%	NA
Indica I	595	80.70%	8.60%	10.76%	0.00%	NA
Indica II	465	79.40%	9.00%	11.61%	0.00%	NA
Indica III	913	76.50%	7.00%	16.54%	0.00%	NA
Indica Intermediate	786	71.90%	16.90%	11.20%	0.00%	NA
Temperate Japonica	767	0.50%	99.00%	0.00%	0.52%	NA
Tropical Japonica	504	0.40%	99.60%	0.00%	0.00%	NA
Japonica Intermediate	241	0.80%	98.30%	0.83%	0.00%	NA
VI/Aromatic	96	2.10%	91.70%	6.25%	0.00%	NA
Intermediate	90	34.40%	53.30%	10.00%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0716100091	C -> DEL	LOC_Os07g27550.1	N	frameshift_variant	Average:15.325; most accessible tissue: Zhenshan97 root, score: 23.888	N	N	N	N
vg0716100091	C -> T	LOC_Os07g27550.1	synonymous_variant ; p.Ala172Ala; LOW	synonymous_codon	Average:15.325; most accessible tissue: Zhenshan97 root, score: 23.888	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0716100091	2.33E-06	8.43E-07	mr1159_2	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