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Detailed information for vg1222907108:

Variant ID: vg1222907108 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 22907108
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCAGCCGCTCCTCCTCCTCCCCCTCGCACGTGCGTTGCGCGTGCGCCACGCTCGAGAGAGAGAGCGCCCACTCTCTTCTCATCCTCGCTCTCTCTCTCTC[T/C]
GTTTCTCTCTCTCTCCGTTTCTCTCTCTCCCCCGTAGAAGCTCCCCCACCGGCGCCGATTTCCCGCCGCCGCCGTTCGAAATCCGGCCGCTCCCTCGCAT

Reverse complement sequence

ATGCGAGGGAGCGGCCGGATTTCGAACGGCGGCGGCGGGAAATCGGCGCCGGTGGGGGAGCTTCTACGGGGGAGAGAGAGAAACGGAGAGAGAGAGAAAC[A/G]
GAGAGAGAGAGAGCGAGGATGAGAAGAGAGTGGGCGCTCTCTCTCTCGAGCGTGGCGCACGCGCAACGCACGTGCGAGGGGGAGGAGGAGGAGCGGCTGA

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	50.00%	0.10%	15.09%	34.77%	NA
All Indica	2759	23.50%	0.20%	22.62%	53.75%	NA
All Japonica	1512	96.30%	0.10%	2.12%	1.52%	NA
Aus	269	38.30%	0.00%	18.22%	43.49%	NA
Indica I	595	60.80%	0.00%	11.43%	27.73%	NA
Indica II	465	8.60%	0.00%	13.55%	77.85%	NA
Indica III	913	12.20%	0.20%	33.84%	53.78%	NA
Indica Intermediate	786	17.00%	0.40%	23.41%	59.16%	NA
Temperate Japonica	767	96.00%	0.00%	1.96%	2.09%	NA
Tropical Japonica	504	98.40%	0.00%	0.60%	0.99%	NA
Japonica Intermediate	241	92.90%	0.40%	5.81%	0.83%	NA
VI/Aromatic	96	89.60%	0.00%	3.12%	7.29%	NA
Intermediate	90	80.00%	0.00%	5.56%	14.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1222907108	T -> C	LOC_Os12g37310-LOC_Os12g37320	intergenic_region ; MODIFIER	silent_mutation	Average:17.449; most accessible tissue: Minghui63 root, score: 23.574	N	N	N	N
vg1222907108	T -> DEL	N	N	silent_mutation	Average:17.449; most accessible tissue: Minghui63 root, score: 23.574	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1222907108	2.99E-06	2.99E-06	mr1595	Jap_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