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Detailed information for vg1216535929:

Variant ID: vg1216535929 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 16535929
Reference Allele: A	Alternative Allele: T
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GAGAAGAGGAGGAGGAAGGGGGAGAGGAGTGTACAGGGGGGATGGGGTTCCCGCAGAAGGTGACTTTTTCACCGGGGTTTTCCACCAACGAAAAGAACGA[A/T]
CAACTGGCAGGGCAACTTTGCGAGGCTATCAACTTTGTATTGATTTAATTACAATCAATACAATGATATAATCGGGATCGTAGATTGGATAATTATTTTT

Reverse complement sequence

AAAAATAATTATCCAATCTACGATCCCGATTATATCATTGTATTGATTGTAATTAAATCAATACAAAGTTGATAGCCTCGCAAAGTTGCCCTGCCAGTTG[T/A]
TCGTTCTTTTCGTTGGTGGAAAACCCCGGTGAAAAAGTCACCTTCTGCGGGAACCCCATCCCCCCTGTACACTCCTCTCCCCCTTCCTCCTCCTCTTCTC

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	86.60%	7.90%	4.93%	0.59%	NA
All Indica	2759	90.30%	0.40%	8.34%	1.01%	NA
All Japonica	1512	77.70%	22.20%	0.07%	0.00%	NA
Aus	269	92.20%	7.80%	0.00%	0.00%	NA
Indica I	595	74.60%	0.20%	23.19%	2.02%	NA
Indica II	465	92.30%	0.40%	5.59%	1.72%	NA
Indica III	913	98.40%	0.00%	1.31%	0.33%	NA
Indica Intermediate	786	91.60%	0.90%	6.87%	0.64%	NA
Temperate Japonica	767	83.80%	16.20%	0.00%	0.00%	NA
Tropical Japonica	504	75.00%	24.80%	0.20%	0.00%	NA
Japonica Intermediate	241	63.90%	36.10%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	90.00%	7.80%	2.22%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1216535929	A -> DEL	N	N	silent_mutation	Average:36.307; most accessible tissue: Zhenshan97 panicle, score: 46.362	N	N	N	N
vg1216535929	A -> T	LOC_Os12g28040.1	downstream_gene_variant ; 1626.0bp to feature; MODIFIER	silent_mutation	Average:36.307; most accessible tissue: Zhenshan97 panicle, score: 46.362	N	N	N	N
vg1216535929	A -> T	LOC_Os12g28020-LOC_Os12g28040	intergenic_region ; MODIFIER	silent_mutation	Average:36.307; most accessible tissue: Zhenshan97 panicle, score: 46.362	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1216535929	1.68E-07	NA	mr1071_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
vg1216535929	NA	1.79E-06	mr1071_2	Jap_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
vg1216535929	1.04E-07	NA	mr1080_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
vg1216535929	NA	1.96E-06	mr1080_2	Jap_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
vg1216535929	7.91E-08	NA	mr1203_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
vg1216535929	NA	3.65E-06	mr1203_2	Jap_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
vg1216535929	9.07E-07	NA	mr1613_2	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
vg1216535929	8.53E-06	NA	mr1613_2	Jap_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
vg1216535929	NA	1.78E-06	mr1617_2	Jap_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