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Detailed information for vg1222221868:

Variant ID: vg1222221868 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 22221868
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CAAGAAGCAGCCGATAGAGCTAAATTGATATGCTAAGACTAGATTAACAGAGACATATGATAAATAGGTAGGCAAGTATATCATCCAAACCAGAGCAATC[T/C]
AAGAGGTCGAATGTCCTGATGCAGCCTTGAACGACGCCGACGTAGACGATATAATTGCCTGGGCCGACGGAACATTGGACTTACCCCTTAGCCGGAGATC

Reverse complement sequence

GATCTCCGGCTAAGGGGTAAGTCCAATGTTCCGTCGGCCCAGGCAATTATATCGTCTACGTCGGCGTCGTTCAAGGCTGCATCAGGACATTCGACCTCTT[A/G]
GATTGCTCTGGTTTGGATGATATACTTGCCTACCTATTTATCATATGTCTCTGTTAATCTAGTCTTAGCATATCAATTTAGCTCTATCGGCTGCTTCTTG

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	16.90%	3.40%	1.50%	78.14%	NA
All Indica	2759	3.50%	2.20%	1.96%	92.35%	NA
All Japonica	1512	44.80%	0.40%	0.73%	54.10%	NA
Aus	269	0.70%	32.30%	1.49%	65.43%	NA
Indica I	595	4.50%	0.20%	1.34%	93.95%	NA
Indica II	465	5.20%	0.00%	2.80%	92.04%	NA
Indica III	913	1.60%	4.50%	0.99%	92.88%	NA
Indica Intermediate	786	3.80%	2.40%	3.05%	90.71%	NA
Temperate Japonica	767	73.30%	0.30%	0.65%	25.81%	NA
Tropical Japonica	504	12.10%	0.40%	0.99%	86.51%	NA
Japonica Intermediate	241	22.40%	0.80%	0.41%	76.35%	NA
VI/Aromatic	96	0.00%	8.30%	0.00%	91.67%	NA
Intermediate	90	26.70%	1.10%	2.22%	70.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1222221868	T -> C	LOC_Os12g36270.1	downstream_gene_variant ; 2890.0bp to feature; MODIFIER	silent_mutation	Average:9.799; most accessible tissue: Minghui63 root, score: 21.615	N	N	N	N
vg1222221868	T -> C	LOC_Os12g36300.1	downstream_gene_variant ; 4342.0bp to feature; MODIFIER	silent_mutation	Average:9.799; most accessible tissue: Minghui63 root, score: 21.615	N	N	N	N
vg1222221868	T -> C	LOC_Os12g36270-LOC_Os12g36300	intergenic_region ; MODIFIER	silent_mutation	Average:9.799; most accessible tissue: Minghui63 root, score: 21.615	N	N	N	N
vg1222221868	T -> DEL	N	N	silent_mutation	Average:9.799; most accessible tissue: Minghui63 root, score: 21.615	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1222221868	1.70E-06	1.70E-06	mr1812	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