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Detailed information for vg1221140689:

Variant ID: vg1221140689 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 21140689
Reference Allele: A	Alternative Allele: T
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TAGAACAAGTGCAAGTGACAGTTCAATGTTTCTTGCATGGGTGATGGATAAATGTTGGCGGGGAGGATTAAGGAATCTGCAACACTGCGTGGGCTCGACA[A/T]
TGATGTGTGGCACTTGCACTGTCCGGCGTCTATGGGTCTCTCTCAGCATATTGCATTCCCCAGCTGAAGGTTCCCTGCCATGAATTCAGAGAAGAAACAA

Reverse complement sequence

TTGTTTCTTCTCTGAATTCATGGCAGGGAACCTTCAGCTGGGGAATGCAATATGCTGAGAGAGACCCATAGACGCCGGACAGTGCAAGTGCCACACATCA[T/A]
TGTCGAGCCCACGCAGTGTTGCAGATTCCTTAATCCTCCCCGCCAACATTTATCCATCACCCATGCAAGAAACATTGAACTGTCACTTGCACTTGTTCTA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	61.30%	11.50%	0.80%	26.39%	NA
All Indica	2759	46.60%	11.40%	1.20%	40.81%	NA
All Japonica	1512	97.80%	0.90%	0.00%	1.26%	NA
Aus	269	14.10%	52.40%	1.49%	31.97%	NA
Indica I	595	77.60%	3.00%	1.01%	18.32%	NA
Indica II	465	24.70%	4.10%	1.94%	69.25%	NA
Indica III	913	35.00%	20.30%	0.99%	43.70%	NA
Indica Intermediate	786	49.50%	11.70%	1.15%	37.66%	NA
Temperate Japonica	767	98.70%	0.70%	0.00%	0.65%	NA
Tropical Japonica	504	97.00%	0.60%	0.00%	2.38%	NA
Japonica Intermediate	241	96.70%	2.50%	0.00%	0.83%	NA
VI/Aromatic	96	31.20%	63.50%	0.00%	5.21%	NA
Intermediate	90	71.10%	15.60%	1.11%	12.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1221140689	A -> DEL	N	N	silent_mutation	Average:43.22; most accessible tissue: Zhenshan97 young leaf, score: 74.302	N	N	N	N
vg1221140689	A -> T	LOC_Os12g34802.1	3_prime_UTR_variant ; 1194.0bp to feature; MODIFIER	silent_mutation	Average:43.22; most accessible tissue: Zhenshan97 young leaf, score: 74.302	N	N	N	N
vg1221140689	A -> T	LOC_Os12g34796.1	downstream_gene_variant ; 2510.0bp to feature; MODIFIER	silent_mutation	Average:43.22; most accessible tissue: Zhenshan97 young leaf, score: 74.302	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1221140689	1.20E-06	1.20E-06	mr1381	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
vg1221140689	NA	4.47E-06	mr1923	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