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Detailed information for vg1209004353:

Variant ID: vg1209004353 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 9004353
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.60, T: 0.40, others allele: 0.00, population size: 58. )

Flanking Sequence (100 bp) in Reference Genome:

GTAGCCGATGTGTGGAGAAAGTCGTCCATCAATCCCAATAAAAACACCAGTCGGCGGCGATGGCAGCCGCCGGAAGTGAAGACATGGTCGCCATCAACAA[C/T]
GGCAGCGGATTACACCAACCGTGGAGGCGAAGAAACCGGTCGGCAGTGATGACGGCGGCCAGCGATGAAGGTGTAGATGCCCAACAACGGTGGTGTGACC

Reverse complement sequence

GGTCACACCACCGTTGTTGGGCATCTACACCTTCATCGCTGGCCGCCGTCATCACTGCCGACCGGTTTCTTCGCCTCCACGGTTGGTGTAATCCGCTGCC[G/A]
TTGTTGATGGCGACCATGTCTTCACTTCCGGCGGCTGCCATCGCCGCCGACTGGTGTTTTTATTGGGATTGATGGACGACTTTCTCCACACATCGGCTAC

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	39.80%	38.10%	0.53%	21.58%	NA
All Indica	2759	54.00%	10.40%	0.87%	34.69%	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	36.10%	21.30%	1.51%	41.01%	NA
Indica II	465	51.80%	12.50%	0.65%	35.05%	NA
Indica III	913	65.30%	2.50%	0.22%	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
vg1209004353	C -> DEL	LOC_Os12g15770.1	N	frameshift_variant	Average:39.365; most accessible tissue: Zhenshan97 young leaf, score: 68.794	N	N	N	N
vg1209004353	C -> T	LOC_Os12g15770.1	synonymous_variant ; p.Pro95Pro; LOW	synonymous_codon	Average:39.365; most accessible tissue: Zhenshan97 young leaf, score: 68.794	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1209004353	NA	2.05E-08	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
vg1209004353	NA	7.24E-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
vg1209004353	NA	3.38E-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