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Detailed information for vg1204022316:

Variant ID: vg1204022316 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 4022316
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CCACTCAATGCTCCTGGTTACATAAAAATACCAGGCGGGCCTAGGACTGAAAGGAGAAGAGAAATGCATGAACCTCCCAAGCCAACAAATTTGTCAAGTC[C/T]
AGTTGTGCCAAGCACAGTTCTGCAGGGTCAGTCCCAGATGGTTCTCAACCAGTGTCATCTCCAAGTCATCAGATGGTGCTGTCTAACACAGCAGGGATCC

Reverse complement sequence

GGATCCCTGCTGTGTTAGACAGCACCATCTGATGACTTGGAGATGACACTGGTTGAGAACCATCTGGGACTGACCCTGCAGAACTGTGCTTGGCACAACT[G/A]
GACTTGACAAATTTGTTGGCTTGGGAGGTTCATGCATTTCTCTTCTCCTTTCAGTCCTAGGCCCGCCTGGTATTTTTATGTAACCAGGAGCATTGAGTGG

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	27.70%	6.50%	0.25%	65.51%	NA
All Indica	2759	7.20%	0.40%	0.18%	92.13%	NA
All Japonica	1512	62.60%	19.20%	0.20%	17.99%	NA
Aus	269	11.20%	0.00%	1.49%	87.36%	NA
Indica I	595	1.80%	0.20%	0.17%	97.82%	NA
Indica II	465	17.60%	0.60%	0.22%	81.51%	NA
Indica III	913	4.50%	0.10%	0.22%	95.18%	NA
Indica Intermediate	786	8.40%	0.90%	0.13%	90.59%	NA
Temperate Japonica	767	83.20%	12.00%	0.39%	4.43%	NA
Tropical Japonica	504	42.10%	26.40%	0.00%	31.55%	NA
Japonica Intermediate	241	40.20%	27.00%	0.00%	32.78%	NA
VI/Aromatic	96	85.40%	0.00%	0.00%	14.58%	NA
Intermediate	90	55.60%	7.80%	0.00%	36.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1204022316	C -> DEL	N	N	silent_mutation	Average:12.098; most accessible tissue: Callus, score: 64.12	N	N	N	N
vg1204022316	C -> T	LOC_Os12g07910.1	downstream_gene_variant ; 2849.0bp to feature; MODIFIER	silent_mutation	Average:12.098; most accessible tissue: Callus, score: 64.12	N	N	N	N
vg1204022316	C -> T	LOC_Os12g07920.1	downstream_gene_variant ; 908.0bp to feature; MODIFIER	silent_mutation	Average:12.098; most accessible tissue: Callus, score: 64.12	N	N	N	N
vg1204022316	C -> T	LOC_Os12g07930.1	downstream_gene_variant ; 368.0bp to feature; MODIFIER	silent_mutation	Average:12.098; most accessible tissue: Callus, score: 64.12	N	N	N	N
vg1204022316	C -> T	LOC_Os12g07920-LOC_Os12g07930	intergenic_region ; MODIFIER	silent_mutation	Average:12.098; most accessible tissue: Callus, score: 64.12	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1204022316	5.84E-07	NA	mr1203	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
vg1204022316	NA	2.35E-07	mr1554	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