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Detailed information for vg1109788044:

Variant ID: vg1109788044 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 9788044
Reference Allele: G	Alternative Allele: C
Primary Allele: G	Secondary Allele: C

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 232. )

Flanking Sequence (100 bp) in Reference Genome:

GTCCTACTTGTTCACTTGCTTCGCTTTCACGCAGACGAAAGAACACGATATTGAGCATCAAGACTAGATGTTCTTGAGTAACTCGGACACGGCCTTCCAG[G/C]
ACTCGGAGAAGACCAAGCTCTTGCGGGTGGTGACGTAGGCCTCGCCGTCGCGCTCGTCACCGAAGACCTCTTTGATCATGTTAATGGCATGGCCCTTCAG

Reverse complement sequence

CTGAAGGGCCATGCCATTAACATGATCAAAGAGGTCTTCGGTGACGAGCGCGACGGCGAGGCCTACGTCACCACCCGCAAGAGCTTGGTCTTCTCCGAGT[C/G]
CTGGAAGGCCGTGTCCGAGTTACTCAAGAACATCTAGTCTTGATGCTCAATATCGTGTTCTTTCGTCTGCGTGAAAGCGAAGCAAGTGAACAAGTAGGAC

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	89.30%	10.60%	0.04%	0.00%	NA
All Indica	2759	82.70%	17.30%	0.07%	0.00%	NA
All Japonica	1512	99.50%	0.50%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	92.80%	7.10%	0.17%	0.00%	NA
Indica II	465	49.00%	51.00%	0.00%	0.00%	NA
Indica III	913	93.90%	6.00%	0.11%	0.00%	NA
Indica Intermediate	786	81.90%	18.10%	0.00%	0.00%	NA
Temperate Japonica	767	99.30%	0.70%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.80%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	78.90%	21.10%	0.00%	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
vg1109788044	G -> C	LOC_Os11g17580.1	missense_variant ; p.Ser224Cys; MODERATE	nonsynonymous_codon ; S224C	Average:70.889; most accessible tissue: Callus, score: 85.41	unknown	unknown	DELETERIOUS	0.00

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1109788044	NA	6.74E-06	mr1154	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
vg1109788044	NA	3.59E-06	mr1050_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
vg1109788044	NA	1.89E-06	mr1097_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
vg1109788044	NA	2.37E-09	mr1154_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