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Detailed information for vg0617527186:

Variant ID: vg0617527186 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 17527186
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 35. )

Flanking Sequence (100 bp) in Reference Genome:

ATGAACCGGCCTTATCCATTAAATATGGGTTGGTCTTGCCCTATATAGGCCCTTCTCCACGTCTAACTCGGGATAGAAACCAAAGGAAACACGAAACCTG[C/T]
CTTCCTGAGCAAGGAAACCTGAGACCCGACGAAAACAGACTCGGACTCGGACCCTGACGGTCTGACTGTCCACATACCTGCGGTCAGACCGGCCCTACAA

Reverse complement sequence

TTGTAGGGCCGGTCTGACCGCAGGTATGTGGACAGTCAGACCGTCAGGGTCCGAGTCCGAGTCTGTTTTCGTCGGGTCTCAGGTTTCCTTGCTCAGGAAG[G/A]
CAGGTTTCGTGTTTCCTTTGGTTTCTATCCCGAGTTAGACGTGGAGAAGGGCCTATATAGGGCAAGACCAACCCATATTTAATGGATAAGGCCGGTTCAT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	92.10%	4.80%	1.18%	1.90%	NA
All Indica	2759	90.20%	7.60%	1.81%	0.36%	NA
All Japonica	1512	97.80%	0.70%	0.07%	1.52%	NA
Aus	269	98.50%	0.00%	0.74%	0.74%	NA
Indica I	595	97.00%	0.00%	2.86%	0.17%	NA
Indica II	465	91.20%	7.30%	1.51%	0.00%	NA
Indica III	913	85.30%	13.60%	0.99%	0.11%	NA
Indica Intermediate	786	90.20%	6.60%	2.16%	1.02%	NA
Temperate Japonica	767	95.80%	1.20%	0.13%	2.87%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.40%	0.00%	0.41%	NA
VI/Aromatic	96	41.70%	1.00%	3.12%	54.17%	NA
Intermediate	90	90.00%	6.70%	0.00%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0617527186	C -> T	LOC_Os06g30340.1	upstream_gene_variant ; 3041.0bp to feature; MODIFIER	silent_mutation	Average:42.077; most accessible tissue: Zhenshan97 flower, score: 65.164	N	N	N	N
vg0617527186	C -> T	LOC_Os06g30340-LOC_Os06g30350	intergenic_region ; MODIFIER	silent_mutation	Average:42.077; most accessible tissue: Zhenshan97 flower, score: 65.164	N	N	N	N
vg0617527186	C -> DEL	N	N	silent_mutation	Average:42.077; most accessible tissue: Zhenshan97 flower, score: 65.164	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0617527186	4.51E-06	1.02E-10	mr1090	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
vg0617527186	NA	9.38E-07	mr1111	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
vg0617527186	8.27E-06	9.23E-09	mr1121	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
vg0617527186	NA	5.46E-08	mr1122	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
vg0617527186	9.42E-06	NA	mr1144	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
vg0617527186	2.63E-06	5.03E-11	mr1211	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
vg0617527186	2.60E-06	NA	mr1068_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
vg0617527186	5.81E-08	2.04E-10	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
vg0617527186	2.16E-07	NA	mr1111_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
vg0617527186	5.96E-07	4.51E-09	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
vg0617527186	7.57E-08	NA	mr1144_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
vg0617527186	4.52E-08	2.96E-12	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
vg0617527186	NA	3.65E-08	mr1632_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