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Detailed information for vg1218135022:

Variant ID: vg1218135022 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 18135022
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGATGACTGCTTTCCTCCACCACCTCCAAAATCCACCACAACATAATGCTCCACCACCACCCCCACAACACTCTAAACTCGCCGAGTTCCTCCGTATCCG[C/T]
CCACCTACCTTCTCTAGCTCCAACAACCCCGTGGATGCGTTGGATTGGTTTCATGCCGTGGGGAAAAAGCTAGACACGGTGCAGTGCAGCGATGAGGAGA

Reverse complement sequence

TCTCCTCATCGCTGCACTGCACCGTGTCTAGCTTTTTCCCCACGGCATGAAACCAATCCAACGCATCCACGGGGTTGTTGGAGCTAGAGAAGGTAGGTGG[G/A]
CGGATACGGAGGAACTCGGCGAGTTTAGAGTGTTGTGGGGGTGGTGGTGGAGCATTATGTTGTGGTGGATTTTGGAGGTGGTGGAGGAAAGCAGTCATCA

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	49.40%	1.40%	20.69%	28.57%	NA
All Indica	2759	50.00%	2.00%	14.32%	33.71%	NA
All Japonica	1512	44.00%	0.60%	32.67%	22.69%	NA
Aus	269	71.70%	0.40%	7.43%	20.45%	NA
Indica I	595	28.60%	0.70%	9.08%	61.68%	NA
Indica II	465	48.40%	9.00%	18.71%	23.87%	NA
Indica III	913	68.00%	0.20%	15.33%	16.43%	NA
Indica Intermediate	786	46.20%	0.90%	14.50%	38.42%	NA
Temperate Japonica	767	67.80%	0.50%	9.91%	21.77%	NA
Tropical Japonica	504	10.10%	0.20%	63.10%	26.59%	NA
Japonica Intermediate	241	39.40%	1.70%	41.49%	17.43%	NA
VI/Aromatic	96	44.80%	0.00%	46.88%	8.33%	NA
Intermediate	90	57.80%	0.00%	26.67%	15.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1218135022	C -> DEL	LOC_Os12g30214.1	N	frameshift_variant	Average:8.761; most accessible tissue: Minghui63 young leaf, score: 14.915	N	N	N	N
vg1218135022	C -> T	LOC_Os12g30214.1	synonymous_variant ; p.Arg408Arg; LOW	synonymous_codon	Average:8.761; most accessible tissue: Minghui63 young leaf, score: 14.915	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1218135022	2.04E-06	2.36E-09	mr1668_2	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