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Detailed information for vg1223453865:

Variant ID: vg1223453865 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 23453865
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.66, C: 0.34, others allele: 0.00, population size: 59. )

Flanking Sequence (100 bp) in Reference Genome:

CCCGTAGCAATCTCTCACACCGCGACTTCCATTGGTGCTAGAGAGATAATTCTACGCGCTGGTTCTCGAACCAGTAAACCCGTAGCAATCGCTCACACCG[T/C]
GACTTCCATTGGTGCTAGAGAGATAATTCTATGCGCTGGTCCTCGAACCAGCAAACCCGTAGCAATCTCTCACGCTGCGACTTCCATTGGTGCTAGAGAT

Reverse complement sequence

ATCTCTAGCACCAATGGAAGTCGCAGCGTGAGAGATTGCTACGGGTTTGCTGGTTCGAGGACCAGCGCATAGAATTATCTCTCTAGCACCAATGGAAGTC[A/G]
CGGTGTGAGCGATTGCTACGGGTTTACTGGTTCGAGAACCAGCGCGTAGAATTATCTCTCTAGCACCAATGGAAGTCGCGGTGTGAGAGATTGCTACGGG

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	52.00%	40.00%	2.88%	5.12%	NA
All Indica	2759	84.80%	5.10%	1.52%	8.52%	NA
All Japonica	1512	0.60%	99.00%	0.00%	0.40%	NA
Aus	269	28.60%	39.40%	31.97%	0.00%	NA
Indica I	595	93.80%	4.90%	1.34%	0.00%	NA
Indica II	465	56.30%	7.50%	2.15%	33.98%	NA
Indica III	913	96.70%	2.30%	0.00%	0.99%	NA
Indica Intermediate	786	81.20%	7.10%	3.05%	8.65%	NA
Temperate Japonica	767	0.30%	99.00%	0.00%	0.78%	NA
Tropical Japonica	504	1.20%	98.80%	0.00%	0.00%	NA
Japonica Intermediate	241	0.40%	99.60%	0.00%	0.00%	NA
VI/Aromatic	96	6.20%	88.50%	4.17%	1.04%	NA
Intermediate	90	28.90%	66.70%	4.44%	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
vg1223453865	T -> C	LOC_Os12g38190.1	missense_variant ; p.Val322Ala; MODERATE	nonsynonymous_codon ; V322A	Average:24.709; most accessible tissue: Zhenshan97 flag leaf, score: 42.807	unknown	unknown	TOLERATED	0.16
vg1223453865	T -> DEL	LOC_Os12g38190.1	N	frameshift_variant	Average:24.709; most accessible tissue: Zhenshan97 flag leaf, score: 42.807	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1223453865	2.21E-06	NA	mr1008	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
vg1223453865	1.98E-06	NA	mr1009	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
vg1223453865	NA	8.17E-06	mr1074	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
vg1223453865	NA	3.81E-07	mr1130	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
vg1223453865	NA	3.47E-13	mr1149	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
vg1223453865	5.01E-09	6.62E-10	mr1672	Ind_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
vg1223453865	NA	4.85E-07	mr1750	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
vg1223453865	NA	3.24E-09	mr1222_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
vg1223453865	NA	2.73E-06	mr1227_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