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Detailed information for vg1222385548:

Variant ID: vg1222385548 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 22385548
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGCCCCGACCCGCGCCATTTGAGGCTGGGACCTGGGCACGAGCCCTTGTTCAAGCCAAGATGCAGAAGGACCGCGGCACAGACCATCCTTGTCTCATACA[C/T]
GCAACAAATAGAATTGACACAGAAATTTCCTCTTTATTTGATTGCAGATTAAATTAGTCTATACAAGAAGGGGGCCCGAAGGCCTTGGAAGAAGAAAGAA

Reverse complement sequence

TTCTTTCTTCTTCCAAGGCCTTCGGGCCCCCTTCTTGTATAGACTAATTTAATCTGCAATCAAATAAAGAGGAAATTTCTGTGTCAATTCTATTTGTTGC[G/A]
TGTATGAGACAAGGATGGTCTGTGCCGCGGTCCTTCTGCATCTTGGCTTGAACAAGGGCTCGTGCCCAGGTCCCAGCCTCAAATGGCGCGGGTCGGGGCT

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	90.00%	5.00%	2.16%	2.90%	NA
All Indica	2759	87.80%	8.00%	3.23%	0.98%	NA
All Japonica	1512	91.40%	0.60%	0.73%	7.28%	NA
Aus	269	99.30%	0.70%	0.00%	0.00%	NA
Indica I	595	93.30%	2.70%	3.87%	0.17%	NA
Indica II	465	75.70%	20.90%	2.58%	0.86%	NA
Indica III	913	92.40%	3.30%	2.96%	1.31%	NA
Indica Intermediate	786	85.50%	9.80%	3.44%	1.27%	NA
Temperate Japonica	767	89.40%	0.30%	0.13%	10.17%	NA
Tropical Japonica	504	93.30%	1.40%	1.59%	3.77%	NA
Japonica Intermediate	241	93.80%	0.00%	0.83%	5.39%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	94.40%	3.30%	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
vg1222385548	C -> DEL	N	N	silent_mutation	Average:15.505; most accessible tissue: Callus, score: 34.864	N	N	N	N
vg1222385548	C -> T	LOC_Os12g36550.1	downstream_gene_variant ; 507.0bp to feature; MODIFIER	silent_mutation	Average:15.505; most accessible tissue: Callus, score: 34.864	N	N	N	N
vg1222385548	C -> T	LOC_Os12g36560.1	downstream_gene_variant ; 134.0bp to feature; MODIFIER	silent_mutation	Average:15.505; most accessible tissue: Callus, score: 34.864	N	N	N	N
vg1222385548	C -> T	LOC_Os12g36570.1	downstream_gene_variant ; 4288.0bp to feature; MODIFIER	silent_mutation	Average:15.505; most accessible tissue: Callus, score: 34.864	N	N	N	N
vg1222385548	C -> T	LOC_Os12g36550-LOC_Os12g36560	intergenic_region ; MODIFIER	silent_mutation	Average:15.505; most accessible tissue: Callus, score: 34.864	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1222385548	3.13E-08	1.79E-09	mr1120	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