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Detailed information for vg0618817199:

Variant ID: vg0618817199 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 18817199
Reference Allele: G	Alternative Allele: C
Primary Allele: G	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGACCCTAGGGATAAACTACACTGGGAACGGCATAGGAGCGGCGGTTGCCGGCGAACCACGGCACAATAATGCAAATGGAGGGCACCGGGAGAAAGAGGA[G/C]
GCAATGGCGATGCTTACCAACACTTAAACAGCGATGAACGGCGAAGGAGATGGCCGGCGACGAGATTGGGACGGCGGCGAGGTTCGGGTCCACGGCGGCG

Reverse complement sequence

CGCCGCCGTGGACCCGAACCTCGCCGCCGTCCCAATCTCGTCGCCGGCCATCTCCTTCGCCGTTCATCGCTGTTTAAGTGTTGGTAAGCATCGCCATTGC[C/G]
TCCTCTTTCTCCCGGTGCCCTCCATTTGCATTATTGTGCCGTGGTTCGCCGGCAACCGCCGCTCCTATGCCGTTCCCAGTGTAGTTTATCCCTAGGGTCT

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	83.70%	7.60%	5.14%	3.55%	NA
All Indica	2759	77.70%	12.80%	8.01%	1.45%	NA
All Japonica	1512	90.50%	0.20%	1.06%	8.20%	NA
Aus	269	98.10%	0.40%	1.49%	0.00%	NA
Indica I	595	77.10%	3.00%	17.65%	2.18%	NA
Indica II	465	84.50%	7.10%	7.96%	0.43%	NA
Indica III	913	74.40%	23.10%	1.75%	0.77%	NA
Indica Intermediate	786	78.10%	11.60%	8.02%	2.29%	NA
Temperate Japonica	767	88.10%	0.40%	0.78%	10.69%	NA
Tropical Japonica	504	94.80%	0.00%	0.99%	4.17%	NA
Japonica Intermediate	241	89.20%	0.00%	2.07%	8.71%	NA
VI/Aromatic	96	96.90%	0.00%	0.00%	3.12%	NA
Intermediate	90	92.20%	4.40%	2.22%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0618817199	G -> C	LOC_Os06g32320.1	upstream_gene_variant ; 4940.0bp to feature; MODIFIER	silent_mutation	Average:62.48; most accessible tissue: Zhenshan97 flag leaf, score: 81.985	N	N	N	N
vg0618817199	G -> C	LOC_Os06g32330.1	upstream_gene_variant ; 50.0bp to feature; MODIFIER	silent_mutation	Average:62.48; most accessible tissue: Zhenshan97 flag leaf, score: 81.985	N	N	N	N
vg0618817199	G -> C	LOC_Os06g32320-LOC_Os06g32330	intergenic_region ; MODIFIER	silent_mutation	Average:62.48; most accessible tissue: Zhenshan97 flag leaf, score: 81.985	N	N	N	N
vg0618817199	G -> DEL	N	N	silent_mutation	Average:62.48; most accessible tissue: Zhenshan97 flag leaf, score: 81.985	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0618817199	7.90E-06	NA	mr1078	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
vg0618817199	2.82E-06	NA	mr1087	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
vg0618817199	9.04E-06	5.52E-10	mr1695	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
vg0618817199	5.95E-06	NA	mr1065_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
vg0618817199	3.12E-06	NA	mr1078_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
vg0618817199	3.84E-09	3.14E-09	mr1087_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
vg0618817199	7.70E-07	2.61E-07	mr1090_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
vg0618817199	5.47E-06	NA	mr1094_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
vg0618817199	NA	5.27E-06	mr1096_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
vg0618817199	8.01E-10	3.58E-08	mr1111_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
vg0618817199	8.55E-06	NA	mr1112_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
vg0618817199	5.06E-06	6.50E-06	mr1121_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
vg0618817199	1.57E-08	4.92E-08	mr1144_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
vg0618817199	6.24E-07	2.52E-07	mr1211_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
vg0618817199	2.08E-06	NA	mr1234_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
vg0618817199	3.35E-07	NA	mr1526_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
vg0618817199	NA	2.20E-07	mr1695_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