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Detailed information for vg0900274248:

Variant ID: vg0900274248 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 274248
Reference Allele: A	Alternative Allele: C
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, others allele: 0.00, population size: 186. )

Flanking Sequence (100 bp) in Reference Genome:

GCACCTTCGAACGCCCTGGCACACAGTTTGATCTCTACAACGTTATTCAGAAATCTGGAAAATCCCTTCGAGATTACATCCGACGCTTTTCTGAACAGCG[A/C]
AACAAGATCTCCGACATCACCGACGATGTCATCATCGCCGCCTTCACCAAAGGAATTCGCCACGAAGAGTTAGTCGGCAAGTTCGGGCACAAACCTCCCA

Reverse complement sequence

TGGGAGGTTTGTGCCCGAACTTGCCGACTAACTCTTCGTGGCGAATTCCTTTGGTGAAGGCGGCGATGATGACATCGTCGGTGATGTCGGAGATCTTGTT[T/G]
CGCTGTTCAGAAAAGCGTCGGATGTAATCTCGAAGGGATTTTCCAGATTTCTGAATAACGTTGTAGAGATCAAACTGTGTGCCAGGGCGTTCGAAGGTGC

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	48.00%	0.70%	7.22%	44.12%	NA
All Indica	2759	30.00%	0.40%	6.13%	63.47%	NA
All Japonica	1512	83.70%	0.00%	1.12%	15.15%	NA
Aus	269	7.10%	7.10%	55.76%	30.11%	NA
Indica I	595	18.70%	0.20%	3.70%	77.48%	NA
Indica II	465	41.90%	0.90%	6.67%	50.54%	NA
Indica III	913	27.90%	0.50%	7.34%	64.18%	NA
Indica Intermediate	786	33.80%	0.30%	6.23%	59.67%	NA
Temperate Japonica	767	70.10%	0.00%	1.96%	27.90%	NA
Tropical Japonica	504	99.40%	0.00%	0.00%	0.60%	NA
Japonica Intermediate	241	94.20%	0.00%	0.83%	4.98%	NA
VI/Aromatic	96	95.80%	0.00%	4.17%	0.00%	NA
Intermediate	90	72.20%	0.00%	1.11%	26.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0900274248	A -> DEL	LOC_Os09g01340.1	N	frameshift_variant	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0900274248	A -> C	LOC_Os09g01340.1	synonymous_variant ; p.Arg526Arg; LOW	synonymous_codon	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0900274248	9.06E-06	3.46E-07	mr1088	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
vg0900274248	NA	1.64E-06	mr1103	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
vg0900274248	NA	4.57E-08	mr1107	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
vg0900274248	NA	2.58E-07	mr1411	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
vg0900274248	NA	4.54E-06	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
vg0900274248	4.94E-06	1.87E-07	mr1620	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
vg0900274248	NA	6.75E-06	mr1878	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