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Detailed information for vg1209694733:

Variant ID: vg1209694733 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 9694733
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.92, T: 0.08, others allele: 0.00, population size: 86. )

Flanking Sequence (100 bp) in Reference Genome:

CGTCACTGAGTGGACTGAGTGCCAAGAAGACATGTGTCATGCCCAGAAATTCACGAACCAGAATTTCGAAGCTGAATGTGCATTAAATCCCTGTCTAGGA[C/T]
CAGCCAGGGTACACAAACGACAATTTTTGACATACAGATCCACGTCTTACAAAAATGGAGATGATTACAAATGCAGCAGAAAAGAAAAACGAGCTAGACT

Reverse complement sequence

AGTCTAGCTCGTTTTTCTTTTCTGCTGCATTTGTAATCATCTCCATTTTTGTAAGACGTGGATCTGTATGTCAAAAATTGTCGTTTGTGTACCCTGGCTG[G/A]
TCCTAGACAGGGATTTAATGCACATTCAGCTTCGAAATTCTGGTTCGTGAATTTCTGGGCATGACACATGTCTTCTTGGCACTCAGTCCACTCAGTGACG

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	48.80%	23.40%	4.66%	23.19%	NA
All Indica	2759	36.40%	22.50%	5.33%	35.77%	NA
All Japonica	1512	79.00%	14.30%	3.57%	3.17%	NA
Aus	269	10.00%	71.70%	2.60%	15.61%	NA
Indica I	595	38.30%	40.00%	7.56%	14.12%	NA
Indica II	465	62.40%	7.30%	3.01%	27.31%	NA
Indica III	913	18.90%	18.20%	4.27%	58.60%	NA
Indica Intermediate	786	39.90%	23.20%	6.23%	30.66%	NA
Temperate Japonica	767	88.30%	5.00%	1.30%	5.48%	NA
Tropical Japonica	504	70.00%	23.80%	5.16%	0.99%	NA
Japonica Intermediate	241	68.00%	24.10%	7.47%	0.41%	NA
VI/Aromatic	96	27.10%	54.20%	6.25%	12.50%	NA
Intermediate	90	57.80%	27.80%	6.67%	7.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1209694733	C -> DEL	LOC_Os12g16900.1	N	frameshift_variant	Average:40.147; most accessible tissue: Minghui63 flag leaf, score: 71.116	N	N	N	N
vg1209694733	C -> T	LOC_Os12g16900.1	missense_variant ; p.Pro972Ser; MODERATE	nonsynonymous_codon ; P972S	Average:40.147; most accessible tissue: Minghui63 flag leaf, score: 71.116	unknown	unknown	DELETERIOUS	0.03

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1209694733	4.22E-06	NA	mr1558_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