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Detailed information for vg0322267088:

Variant ID: vg0322267088 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 22267088
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.94, T: 0.05, others allele: 0.00, population size: 250. )

Flanking Sequence (100 bp) in Reference Genome:

CTCGTGAGGTATCATGTGATACCTATCAGGTATCAGATGACTTCTACCACGTATCAGGTGATACTCGTGAGATATCATGTGATACCTATCAGGTATTAGA[C/T]
GATTTCTACCACGTATCGGGTGATACTTACGAGATATCAGATGATACCTACCGGATATCAGGTGATTCCTACTAGGTATCAGGAGCTGAGCATCGAGGCG

Reverse complement sequence

CGCCTCGATGCTCAGCTCCTGATACCTAGTAGGAATCACCTGATATCCGGTAGGTATCATCTGATATCTCGTAAGTATCACCCGATACGTGGTAGAAATC[G/A]
TCTAATACCTGATAGGTATCACATGATATCTCACGAGTATCACCTGATACGTGGTAGAAGTCATCTGATACCTGATAGGTATCACATGATACCTCACGAG

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	72.40%	27.20%	0.19%	0.23%	NA
All Indica	2759	64.30%	35.10%	0.25%	0.40%	NA
All Japonica	1512	93.50%	6.50%	0.00%	0.00%	NA
Aus	269	27.50%	72.10%	0.37%	0.00%	NA
Indica I	595	83.50%	16.30%	0.17%	0.00%	NA
Indica II	465	92.50%	7.10%	0.00%	0.43%	NA
Indica III	913	46.20%	53.00%	0.22%	0.55%	NA
Indica Intermediate	786	53.90%	45.00%	0.51%	0.51%	NA
Temperate Japonica	767	99.60%	0.40%	0.00%	0.00%	NA
Tropical Japonica	504	94.60%	5.40%	0.00%	0.00%	NA
Japonica Intermediate	241	71.40%	28.60%	0.00%	0.00%	NA
VI/Aromatic	96	93.80%	6.20%	0.00%	0.00%	NA
Intermediate	90	78.90%	20.00%	1.11%	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
vg0322267088	C -> T	LOC_Os03g40080.1	synonymous_variant ; p.Asp753Asp; LOW	synonymous_codon	Average:69.403; most accessible tissue: Zhenshan97 panicle, score: 82.336	N	N	N	N
vg0322267088	C -> DEL	LOC_Os03g40080.1	N	frameshift_variant	Average:69.403; most accessible tissue: Zhenshan97 panicle, score: 82.336	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0322267088	NA	3.14E-07	mr1221	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
vg0322267088	7.29E-07	NA	mr1676	Jap_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
vg0322267088	9.89E-07	NA	mr1676_2	Jap_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