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Detailed information for vg1217487071:

Variant ID: vg1217487071 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 17487071
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 350. )

Flanking Sequence (100 bp) in Reference Genome:

AGGCTAGAAGATGGACATTATACCTTGATGAGGAGCAAGTGAAGACATTGATGATGCGGGGTATGAAGTGGCTATTTATGGCAAAACGGTGAAGGGCAAG[C/T]
AAGGCTCGGCTACAATGGACCATGCGGGGAGAGGCTTGGCACCGATGGACCGAATCCGGTAGTGAAAGGCGAGTGAAGGCTTTGTCATGATGGTCATGAT

Reverse complement sequence

ATCATGACCATCATGACAAAGCCTTCACTCGCCTTTCACTACCGGATTCGGTCCATCGGTGCCAAGCCTCTCCCCGCATGGTCCATTGTAGCCGAGCCTT[G/A]
CTTGCCCTTCACCGTTTTGCCATAAATAGCCACTTCATACCCCGCATCATCAATGTCTTCACTTGCTCCTCATCAAGGTATAATGTCCATCTTCTAGCCT

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	95.90%	3.20%	0.78%	0.08%	NA
All Indica	2759	99.30%	0.60%	0.07%	0.00%	NA
All Japonica	1512	97.70%	0.00%	2.05%	0.26%	NA
Aus	269	49.10%	49.80%	1.12%	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	99.60%	0.40%	0.00%	0.00%	NA
Indica Intermediate	786	98.20%	1.50%	0.25%	0.00%	NA
Temperate Japonica	767	95.60%	0.00%	3.91%	0.52%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.00%	0.41%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	98.90%	0.00%	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
vg1217487071	C -> DEL	LOC_Os12g29434.1	N	frameshift_variant	Average:42.124; most accessible tissue: Minghui63 flag leaf, score: 57.881	N	N	N	N
vg1217487071	C -> T	LOC_Os12g29434.1	stop_gained ; p.Gln306*; HIGH	stop_gained	Average:42.124; most accessible tissue: Minghui63 flag leaf, score: 57.881	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1217487071	8.89E-06	NA	mr1368	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
vg1217487071	NA	9.76E-08	mr1762_2	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