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Detailed information for vg1215726806:

Variant ID: vg1215726806 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 15726806
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 103. )

Flanking Sequence (100 bp) in Reference Genome:

GTTGCCCAATGAGCTCTCTCGCTTGTCGCCCAGATTCCAAGGCGCGCTGCCGTCGATGTTCAGCCTCCTTTGCAATCCGTTCGCGATCTTGTTGCTCACG[C/T]
TGTAGTCGTTCTTGCTCCTGTCGTTGTCGCTCTTCCTCCAGTCGGCGACGTTCAGTTTCTTGCCGTGCGCGCTCTTGGTCCGCTTCTCGGGCTCGGCGCT

Reverse complement sequence

AGCGCCGAGCCCGAGAAGCGGACCAAGAGCGCGCACGGCAAGAAACTGAACGTCGCCGACTGGAGGAAGAGCGACAACGACAGGAGCAAGAACGACTACA[G/A]
CGTGAGCAACAAGATCGCGAACGGATTGCAAAGGAGGCTGAACATCGACGGCAGCGCGCCTTGGAATCTGGGCGACAAGCGAGAGAGCTCATTGGGCAAC

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	73.90%	18.90%	4.23%	2.98%	NA
All Indica	2759	71.00%	17.30%	6.67%	5.07%	NA
All Japonica	1512	78.80%	21.00%	0.20%	0.00%	NA
Aus	269	87.70%	7.40%	4.83%	0.00%	NA
Indica I	595	90.90%	4.00%	3.70%	1.34%	NA
Indica II	465	85.40%	11.60%	1.94%	1.08%	NA
Indica III	913	46.50%	31.80%	11.50%	10.19%	NA
Indica Intermediate	786	75.70%	13.90%	6.11%	4.33%	NA
Temperate Japonica	767	96.10%	3.80%	0.13%	0.00%	NA
Tropical Japonica	504	55.00%	44.80%	0.20%	0.00%	NA
Japonica Intermediate	241	73.90%	25.70%	0.41%	0.00%	NA
VI/Aromatic	96	39.60%	60.40%	0.00%	0.00%	NA
Intermediate	90	74.40%	24.40%	0.00%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1215726806	C -> DEL	LOC_Os12g26840.1	N	frameshift_variant	Average:45.405; most accessible tissue: Zhenshan97 flag leaf, score: 63.101	N	N	N	N
vg1215726806	C -> T	LOC_Os12g26840.1	missense_variant ; p.Ser179Asn; MODERATE	nonsynonymous_codon ; S179N	Average:45.405; most accessible tissue: Zhenshan97 flag leaf, score: 63.101	unknown	unknown	TOLERATED	0.22

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1215726806	3.99E-06	3.99E-06	mr1956_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