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Detailed information for vg0715979176:

Variant ID: vg0715979176 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 15979176
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 127. )

Flanking Sequence (100 bp) in Reference Genome:

TCGGCAGTAAGACTATTCCTACTACGTTTTTTGTCATCGATGGGAAGGGTTCTTACAGTTTGTTGCTCGGAAGGGATTGGATTCACGCCAATTGTTGTAT[T/C]
CCTTCGACTATGCACCAATGCTTAATTCAGTGGCAAGGCGACAAAATAGAGATCGTGCCAGCCGACAGGTCAGTTAATGTTGCCAGTGCCGATTTAGCTC

Reverse complement sequence

GAGCTAAATCGGCACTGGCAACATTAACTGACCTGTCGGCTGGCACGATCTCTATTTTGTCGCCTTGCCACTGAATTAAGCATTGGTGCATAGTCGAAGG[A/G]
ATACAACAATTGGCGTGAATCCAATCCCTTCCGAGCAACAAACTGTAAGAACCCTTCCCATCGATGACAAAAAACGTAGTAGGAATAGTCTTACTGCCGA

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	85.10%	4.40%	2.96%	7.51%	NA
All Indica	2759	75.10%	7.60%	4.89%	12.47%	NA
All Japonica	1512	99.60%	0.00%	0.07%	0.33%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	86.40%	0.20%	1.51%	11.93%	NA
Indica II	465	50.50%	17.60%	9.89%	21.94%	NA
Indica III	913	76.80%	6.40%	6.02%	10.84%	NA
Indica Intermediate	786	79.00%	8.70%	3.18%	9.16%	NA
Temperate Japonica	767	99.50%	0.00%	0.00%	0.52%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.00%	0.41%	0.41%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	87.80%	1.10%	4.44%	6.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0715979176	T -> DEL	LOC_Os07g27420.1	N	frameshift_variant	Average:22.812; most accessible tissue: Zhenshan97 flag leaf, score: 53.795	N	N	N	N
vg0715979176	T -> C	LOC_Os07g27420.1	synonymous_variant ; p.Ile1040Ile; LOW	synonymous_codon	Average:22.812; most accessible tissue: Zhenshan97 flag leaf, score: 53.795	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0715979176	NA	4.09E-07	mr1399_2	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
vg0715979176	NA	7.77E-07	mr1457_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
vg0715979176	NA	3.51E-07	mr1458_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
vg0715979176	NA	5.43E-06	mr1479_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
vg0715979176	NA	4.27E-06	mr1502_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
vg0715979176	NA	8.11E-06	mr1629_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
vg0715979176	NA	8.93E-07	mr1892_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
vg0715979176	NA	4.40E-07	mr1892_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