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Detailed information for vg1214586572:

Variant ID: vg1214586572 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 14586572
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AACATATGAACTTATGACAGTACCTATCTATAAGTTCAAAAACCTTGTCAAACGTAGACTCTTTTTTATCCATTGAGCCATATACGTTGACGGTGCAGGC[C/T]
TCCAGGTCGAAGAGTAAAAGCACCCAGTGGAATCTGCAATGTGCGTGGGATGCATTACATATGAAACACTTAGCATGTTCGTACGGGAATGAAATTTGGT

Reverse complement sequence

ACCAAATTTCATTCCCGTACGAACATGCTAAGTGTTTCATATGTAATGCATCCCACGCACATTGCAGATTCCACTGGGTGCTTTTACTCTTCGACCTGGA[G/A]
GCCTGCACCGTCAACGTATATGGCTCAATGGATAAAAAAGAGTCTACGTTTGACAAGGTTTTTGAACTTATAGATAGGTACTGTCATAAGTTCATATGTT

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	32.30%	10.30%	5.73%	51.67%	NA
All Indica	2759	23.50%	17.10%	8.84%	50.63%	NA
All Japonica	1512	52.60%	0.30%	1.06%	46.03%	NA
Aus	269	14.90%	0.00%	1.49%	83.64%	NA
Indica I	595	50.10%	21.80%	0.67%	27.39%	NA
Indica II	465	14.40%	3.20%	7.74%	74.62%	NA
Indica III	913	11.60%	21.00%	15.66%	51.70%	NA
Indica Intermediate	786	22.40%	17.00%	7.76%	52.80%	NA
Temperate Japonica	767	80.70%	0.00%	1.04%	18.25%	NA
Tropical Japonica	504	17.50%	0.80%	0.99%	80.75%	NA
Japonica Intermediate	241	36.90%	0.00%	1.24%	61.83%	NA
VI/Aromatic	96	9.40%	2.10%	3.12%	85.42%	NA
Intermediate	90	40.00%	8.90%	4.44%	46.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1214586572	C -> DEL	LOC_Os12g25320.1	N	frameshift_variant	Average:28.268; most accessible tissue: Zhenshan97 flower, score: 41.495	N	N	N	N
vg1214586572	C -> T	LOC_Os12g25320.1	synonymous_variant ; p.Glu1446Glu; LOW	synonymous_codon	Average:28.268; most accessible tissue: Zhenshan97 flower, score: 41.495	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1214586572	1.96E-07	1.20E-06	mr1137_2	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