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Detailed information for vg1215554899:

Variant ID: vg1215554899 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 15554899
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CTCATAATTTGAGCAATCATCATTATTAGGAATAAATTTAGATTTAAGATTTAAGAGATTAAATGATAAATTCCTGTTTTCTATACATCTTCTCACACTT[C/T]
TTATTTTTTGCACTCAAAATATTAATAGCTTCCTCAAAAGCACTCACTCTGTGTCAGATTCACCACGCGCCATAAAGCAAACATAGGAGATGTTCTTTCC

Reverse complement sequence

GGAAAGAACATCTCCTATGTTTGCTTTATGGCGCGTGGTGAATCTGACACAGAGTGAGTGCTTTTGAGGAAGCTATTAATATTTTGAGTGCAAAAAATAA[G/A]
AAGTGTGAGAAGATGTATAGAAAACAGGAATTTATCATTTAATCTCTTAAATCTTAAATCTAAATTTATTCCTAATAATGATGATTGCTCAAATTATGAG

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	40.30%	0.10%	6.05%	53.47%	NA
All Indica	2759	22.00%	0.30%	7.43%	70.28%	NA
All Japonica	1512	72.90%	0.00%	2.98%	24.07%	NA
Aus	269	43.50%	0.00%	7.81%	48.70%	NA
Indica I	595	12.60%	0.80%	12.10%	74.45%	NA
Indica II	465	29.50%	0.00%	4.30%	66.24%	NA
Indica III	913	21.80%	0.20%	7.01%	70.97%	NA
Indica Intermediate	786	25.10%	0.00%	6.23%	68.70%	NA
Temperate Japonica	767	94.80%	0.00%	0.26%	4.95%	NA
Tropical Japonica	504	40.90%	0.00%	8.33%	50.79%	NA
Japonica Intermediate	241	70.50%	0.00%	0.41%	29.05%	NA
VI/Aromatic	96	33.30%	0.00%	5.21%	61.46%	NA
Intermediate	90	51.10%	0.00%	11.11%	37.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1215554899	C -> DEL	N	N	silent_mutation	Average:6.186; most accessible tissue: Callus, score: 15.107	N	N	N	N
vg1215554899	C -> T	LOC_Os12g26570.1	upstream_gene_variant ; 4973.0bp to feature; MODIFIER	silent_mutation	Average:6.186; most accessible tissue: Callus, score: 15.107	N	N	N	N
vg1215554899	C -> T	LOC_Os12g26580.1	intron_variant ; MODIFIER	silent_mutation	Average:6.186; most accessible tissue: Callus, score: 15.107	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1215554899	NA	6.54E-06	mr1060	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
vg1215554899	NA	2.51E-07	mr1458_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
vg1215554899	NA	9.64E-07	mr1931_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