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Detailed information for vg1222758888:

Variant ID: vg1222758888 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 22758888
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 236. )

Flanking Sequence (100 bp) in Reference Genome:

ATAGTTTCTACCAAGCGGCCGAAATTAATCTACGCATCACGCCGTCCGCCGCCGCTGCGAGAGTGCGACAACTCTTTGTAGGTTTGTCCTAAAAACCTTC[C/T]
GTTTTGCCCACGAGACGGGTAGTTATCCTCAAATCGATCTAAATCGGCCTAGAGGCTGATTTTGATCTCTAAATCGGCTTTGCTAGCCGGTTTAGCTGTT

Reverse complement sequence

AACAGCTAAACCGGCTAGCAAAGCCGATTTAGAGATCAAAATCAGCCTCTAGGCCGATTTAGATCGATTTGAGGATAACTACCCGTCTCGTGGGCAAAAC[G/A]
GAAGGTTTTTAGGACAAACCTACAAAGAGTTGTCGCACTCTCGCAGCGGCGGCGGACGGCGTGATGCGTAGATTAATTTCGGCCGCTTGGTAGAAACTAT

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	83.10%	0.30%	2.20%	14.35%	NA
All Indica	2759	71.50%	0.50%	3.73%	24.25%	NA
All Japonica	1512	99.70%	0.10%	0.07%	0.20%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	88.40%	0.00%	1.18%	10.42%	NA
Indica II	465	77.20%	1.10%	4.09%	17.63%	NA
Indica III	913	54.80%	0.70%	5.15%	39.43%	NA
Indica Intermediate	786	74.80%	0.40%	3.82%	20.99%	NA
Temperate Japonica	767	99.70%	0.10%	0.13%	0.00%	NA
Tropical Japonica	504	99.40%	0.00%	0.00%	0.60%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	0.00%	0.00%	1.04%	NA
Intermediate	90	94.40%	0.00%	0.00%	5.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1222758888	C -> DEL	N	N	silent_mutation	Average:15.573; most accessible tissue: Minghui63 panicle, score: 29.741	N	N	N	N
vg1222758888	C -> T	LOC_Os12g37140.1	upstream_gene_variant ; 1597.0bp to feature; MODIFIER	silent_mutation	Average:15.573; most accessible tissue: Minghui63 panicle, score: 29.741	N	N	N	N
vg1222758888	C -> T	LOC_Os12g37130-LOC_Os12g37140	intergenic_region ; MODIFIER	silent_mutation	Average:15.573; most accessible tissue: Minghui63 panicle, score: 29.741	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1222758888	8.83E-07	2.55E-07	mr1083	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
vg1222758888	6.58E-07	6.58E-07	mr1926	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