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Detailed information for vg1209004330:

Variant ID: vg1209004330 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 9004330
Reference Allele: G	Alternative Allele: T
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.59, T: 0.41, others allele: 0.00, population size: 61. )

Flanking Sequence (100 bp) in Reference Genome:

GTGTTCCCCCGGTAATAGCAGATGTAGCCGATGTGTGGAGAAAGTCGTCCATCAATCCCAATAAAAACACCAGTCGGCGGCGATGGCAGCCGCCGGAAGT[G/T]
AAGACATGGTCGCCATCAACAACGGCAGCGGATTACACCAACCGTGGAGGCGAAGAAACCGGTCGGCAGTGATGACGGCGGCCAGCGATGAAGGTGTAGA

Reverse complement sequence

TCTACACCTTCATCGCTGGCCGCCGTCATCACTGCCGACCGGTTTCTTCGCCTCCACGGTTGGTGTAATCCGCTGCCGTTGTTGATGGCGACCATGTCTT[C/A]
ACTTCCGGCGGCTGCCATCGCCGCCGACTGGTGTTTTTATTGGGATTGATGGACGACTTTCTCCACACATCGGCTACATCTGCTATTACCGGGGGAACAC

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	39.80%	38.20%	0.51%	21.54%	NA
All Indica	2759	54.10%	10.40%	0.83%	34.61%	NA
All Japonica	1512	4.40%	94.60%	0.00%	0.99%	NA
Aus	269	81.00%	5.20%	0.37%	13.38%	NA
Indica I	595	36.30%	21.50%	1.34%	40.84%	NA
Indica II	465	52.00%	12.70%	0.43%	34.84%	NA
Indica III	913	65.30%	2.40%	0.33%	31.98%	NA
Indica Intermediate	786	55.90%	10.10%	1.27%	32.82%	NA
Temperate Japonica	767	6.00%	93.00%	0.00%	1.04%	NA
Tropical Japonica	504	3.60%	95.80%	0.00%	0.60%	NA
Japonica Intermediate	241	1.20%	97.10%	0.00%	1.66%	NA
VI/Aromatic	96	72.90%	22.90%	0.00%	4.17%	NA
Intermediate	90	36.70%	54.40%	0.00%	8.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1209004330	G -> DEL	LOC_Os12g15770.1	N	frameshift_variant	Average:39.483; most accessible tissue: Minghui63 flag leaf, score: 69.182	N	N	N	N
vg1209004330	G -> T	LOC_Os12g15770.1	stop_gained ; p.Ser103*; HIGH	stop_gained	Average:39.483; most accessible tissue: Minghui63 flag leaf, score: 69.182	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1209004330	NA	9.03E-09	mr1425	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
vg1209004330	NA	2.92E-06	mr1425	Ind_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
vg1209004330	NA	3.19E-06	mr1574	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
vg1209004330	NA	3.50E-08	mr1659	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
vg1209004330	NA	4.06E-06	mr1864_2	Ind_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