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Detailed information for vg1202552737:

Variant ID: vg1202552737 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 2552737
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GCAACTTTACCAAAATTTGGTAAGGTTGAAAATGGCAGCACAGTGAACAGGCCCTACATATCTCACAAAAGTTTTTAAATAAGAAGAACGGTCAAATATG[T/C]
GCTAAAAAGTCAACGGTGTCAAACATTTCGAAACGGAGGGAGTATATATATATATATATATATATATATATATATATATACATACATACATACACACACA

Reverse complement sequence

TGTGTGTGTATGTATGTATGTATATATATATATATATATATATATATATATATATATACTCCCTCCGTTTCGAAATGTTTGACACCGTTGACTTTTTAGC[A/G]
CATATTTGACCGTTCTTCTTATTTAAAAACTTTTGTGAGATATGTAGGGCCTGTTCACTGTGCTGCCATTTTCAACCTTACCAAATTTTGGTAAAGTTGC

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	56.20%	43.60%	0.21%	0.00%	NA
All Indica	2759	91.70%	8.00%	0.29%	0.00%	NA
All Japonica	1512	2.30%	97.70%	0.00%	0.00%	NA
Aus	269	22.30%	77.70%	0.00%	0.00%	NA
Indica I	595	99.00%	0.80%	0.17%	0.00%	NA
Indica II	465	83.20%	16.30%	0.43%	0.00%	NA
Indica III	913	93.10%	6.60%	0.33%	0.00%	NA
Indica Intermediate	786	89.70%	10.10%	0.25%	0.00%	NA
Temperate Japonica	767	3.50%	96.50%	0.00%	0.00%	NA
Tropical Japonica	504	1.40%	98.60%	0.00%	0.00%	NA
Japonica Intermediate	241	0.40%	99.60%	0.00%	0.00%	NA
VI/Aromatic	96	1.00%	99.00%	0.00%	0.00%	NA
Intermediate	90	32.20%	65.60%	2.22%	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
vg1202552737	T -> C	LOC_Os12g05570.1	upstream_gene_variant ; 2427.0bp to feature; MODIFIER	silent_mutation	Average:30.211; most accessible tissue: Zhenshan97 panicle, score: 52.263	N	N	N	N
vg1202552737	T -> C	LOC_Os12g05550.1	downstream_gene_variant ; 4831.0bp to feature; MODIFIER	silent_mutation	Average:30.211; most accessible tissue: Zhenshan97 panicle, score: 52.263	N	N	N	N
vg1202552737	T -> C	LOC_Os12g05560.1	downstream_gene_variant ; 1299.0bp to feature; MODIFIER	silent_mutation	Average:30.211; most accessible tissue: Zhenshan97 panicle, score: 52.263	N	N	N	N
vg1202552737	T -> C	LOC_Os12g05560-LOC_Os12g05570	intergenic_region ; MODIFIER	silent_mutation	Average:30.211; most accessible tissue: Zhenshan97 panicle, score: 52.263	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1202552737	NA	6.83E-06	mr1076	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
vg1202552737	NA	1.12E-06	mr1103	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
vg1202552737	NA	8.92E-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
vg1202552737	NA	8.01E-31	mr1208	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
vg1202552737	NA	1.43E-24	mr1264	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
vg1202552737	NA	1.62E-08	mr1342	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
vg1202552737	NA	2.83E-07	mr1411	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
vg1202552737	NA	6.80E-28	mr1436	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
vg1202552737	NA	7.80E-06	mr1436	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
vg1202552737	NA	1.79E-06	mr1560	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
vg1202552737	NA	3.59E-18	mr1598	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
vg1202552737	NA	7.94E-12	mr1609	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
vg1202552737	NA	6.25E-06	mr1620	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
vg1202552737	NA	2.07E-13	mr1655	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
vg1202552737	NA	1.88E-24	mr1862	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
vg1202552737	NA	5.53E-39	mr1208_2	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
vg1202552737	NA	1.59E-07	mr1548_2	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
vg1202552737	NA	8.92E-10	mr1782_2	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