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Detailed information for vg1122732664:

Variant ID: vg1122732664 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 22732664
Reference Allele: C	Alternative Allele: G
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, G: 0.02, others allele: 0.00, population size: 86. )

Flanking Sequence (100 bp) in Reference Genome:

TCGAATTCCGGCGGCTCCCCGCGGCGGCGGCCGGCGGCGGTGATTTCCGCGTGCGGATGACGGGCTACACCAGGGCTCGGCCGTCGGACCACCACAACCC[C/G]
GACAACACCTACGTGTTCGCCGGCGATGGCCGTGAGCTGCACGAGATCGTCGTGCTCGCCGCCGGCGAGCTGGAGCACAGGTTCGTCGCCGCCGTGAGGC

Reverse complement sequence

GCCTCACGGCGGCGACGAACCTGTGCTCCAGCTCGCCGGCGGCGAGCACGACGATCTCGTGCAGCTCACGGCCATCGCCGGCGAACACGTAGGTGTTGTC[G/C]
GGGTTGTGGTGGTCCGACGGCCGAGCCCTGGTGTAGCCCGTCATCCGCACGCGGAAATCACCGCCGCCGGCCGCCGCCGCGGGGAGCCGCCGGAATTCGA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	50.40%	49.30%	0.32%	0.00%	NA
All Indica	2759	29.50%	70.20%	0.36%	0.00%	NA
All Japonica	1512	91.60%	8.10%	0.26%	0.00%	NA
Aus	269	21.90%	78.10%	0.00%	0.00%	NA
Indica I	595	14.80%	84.70%	0.50%	0.00%	NA
Indica II	465	36.30%	63.40%	0.22%	0.00%	NA
Indica III	913	39.20%	60.40%	0.44%	0.00%	NA
Indica Intermediate	786	25.20%	74.60%	0.25%	0.00%	NA
Temperate Japonica	767	94.10%	5.30%	0.52%	0.00%	NA
Tropical Japonica	504	87.50%	12.50%	0.00%	0.00%	NA
Japonica Intermediate	241	92.10%	7.90%	0.00%	0.00%	NA
VI/Aromatic	96	83.30%	16.70%	0.00%	0.00%	NA
Intermediate	90	51.10%	47.80%	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
vg1122732664	C -> G	LOC_Os11g38380.1	synonymous_variant ; p.Pro287Pro; LOW	synonymous_codon	Average:63.484; most accessible tissue: Minghui63 young leaf, score: 78.054	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1122732664	NA	8.29E-08	mr1066	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
vg1122732664	NA	1.62E-07	mr1220	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
vg1122732664	NA	1.03E-08	mr1275	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
vg1122732664	NA	3.90E-18	mr1304	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
vg1122732664	NA	8.20E-07	mr1511	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
vg1122732664	NA	6.22E-07	mr1622	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
vg1122732664	NA	2.50E-06	mr1679	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
vg1122732664	NA	2.73E-06	mr1691	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
vg1122732664	NA	2.57E-06	mr1693	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
vg1122732664	NA	5.77E-06	mr1720	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
vg1122732664	NA	1.02E-09	mr1835	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
vg1122732664	NA	5.91E-07	mr1886	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
vg1122732664	NA	8.30E-11	mr1904	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
vg1122732664	NA	1.81E-09	mr1986	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
vg1122732664	NA	4.29E-06	mr1310_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