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Detailed information for vg0910273304:

Variant ID: vg0910273304 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 10273304
Reference Allele: G	Alternative Allele: C
Primary Allele: G	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GCGTGTCCAACTTTACCGTGCTACTGATTCTCTATACCTTCGGGAGTGGAGCAAAGACGGCCTGCATCTTCTCCACCTTCACCGGCGCCGACGAGGAGCT[G/C]
CGGCTGCGCCTCACAAGAAGCATGGACCTCGGTGACCTTATCCGGCCCAAGGGCGTCCCAAGGAGACAGAGACATTTCGATGCCGACGCCATGCACTTCG

Reverse complement sequence

CGAAGTGCATGGCGTCGGCATCGAAATGTCTCTGTCTCCTTGGGACGCCCTTGGGCCGGATAAGGTCACCGAGGTCCATGCTTCTTGTGAGGCGCAGCCG[C/G]
AGCTCCTCGTCGGCGCCGGTGAAGGTGGAGAAGATGCAGGCCGTCTTTGCTCCACTCCCGAAGGTATAGAGAATCAGTAGCACGGTAAAGTTGGACACGC

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	40.30%	23.40%	1.10%	35.19%	NA
All Indica	2759	36.90%	2.70%	1.70%	58.72%	NA
All Japonica	1512	40.30%	59.10%	0.26%	0.33%	NA
Aus	269	82.90%	7.80%	0.37%	8.92%	NA
Indica I	595	9.10%	6.70%	2.18%	82.02%	NA
Indica II	465	57.60%	1.90%	1.51%	38.92%	NA
Indica III	913	43.60%	0.50%	1.20%	54.65%	NA
Indica Intermediate	786	37.80%	2.70%	2.04%	57.51%	NA
Temperate Japonica	767	58.90%	40.30%	0.52%	0.26%	NA
Tropical Japonica	504	15.30%	84.10%	0.00%	0.60%	NA
Japonica Intermediate	241	33.60%	66.40%	0.00%	0.00%	NA
VI/Aromatic	96	17.70%	80.20%	0.00%	2.08%	NA
Intermediate	90	41.10%	45.60%	0.00%	13.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0910273304	G -> DEL	LOC_Os09g16810.1	N	frameshift_variant	Average:14.386; most accessible tissue: Callus, score: 65.86	N	N	N	N
vg0910273304	G -> C	LOC_Os09g16810.1	synonymous_variant ; p.Leu217Leu; LOW	synonymous_codon	Average:14.386; most accessible tissue: Callus, score: 65.86	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0910273304	NA	4.25E-11	mr1174	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
vg0910273304	NA	2.23E-06	mr1188	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
vg0910273304	NA	5.71E-06	mr1347	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
vg0910273304	NA	9.00E-07	mr1072_2	Jap_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
vg0910273304	NA	7.51E-06	mr1075_2	Jap_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
vg0910273304	NA	4.53E-08	mr1077_2	Jap_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
vg0910273304	NA	2.25E-10	mr1137_2	Jap_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
vg0910273304	NA	2.84E-06	mr1149_2	Jap_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
vg0910273304	NA	2.88E-09	mr1174_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
vg0910273304	NA	1.49E-06	mr1188_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
vg0910273304	NA	8.53E-06	mr1221_2	Jap_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
vg0910273304	NA	1.06E-07	mr1347_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
vg0910273304	NA	5.73E-07	mr1441_2	Jap_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
vg0910273304	NA	6.42E-07	mr1617_2	Jap_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
vg0910273304	NA	4.64E-06	mr1717_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