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Detailed information for vg0801822513:

Variant ID: vg0801822513 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 1822513
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GGAACAGGAGGAGAAGATTATACCCCGAGAATGGCCCTCCGCTGGATGGTGAGGCAGAATTGCCTCCGTTGTTGTTGTCGTTCACGGCACCTCCTCCTGG[C/T]
GCACTAGCTCCGGCTCCTGTTGGCGGCGCACCACCTCCGCCATCTCCTCCAGCAGCGGCGGCAACTCCAGACATCGCGATGAGCAGTCGTGTGGGAGGCA

Reverse complement sequence

TGCCTCCCACACGACTGCTCATCGCGATGTCTGGAGTTGCCGCCGCTGCTGGAGGAGATGGCGGAGGTGGTGCGCCGCCAACAGGAGCCGGAGCTAGTGC[G/A]
CCAGGAGGAGGTGCCGTGAACGACAACAACAACGGAGGCAATTCTGCCTCACCATCCAGCGGAGGGCCATTCTCGGGGTATAATCTTCTCCTCCTGTTCC

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	52.30%	24.20%	12.19%	11.34%	NA
All Indica	2759	22.40%	39.90%	18.81%	18.85%	NA
All Japonica	1512	98.50%	1.20%	0.13%	0.13%	NA
Aus	269	79.90%	0.40%	17.47%	2.23%	NA
Indica I	595	31.30%	64.90%	2.69%	1.18%	NA
Indica II	465	4.50%	73.30%	3.66%	18.49%	NA
Indica III	913	21.70%	6.60%	41.18%	30.56%	NA
Indica Intermediate	786	27.20%	39.90%	13.99%	18.83%	NA
Temperate Japonica	767	98.30%	1.60%	0.00%	0.13%	NA
Tropical Japonica	504	99.00%	0.60%	0.40%	0.00%	NA
Japonica Intermediate	241	98.30%	1.20%	0.00%	0.41%	NA
VI/Aromatic	96	96.90%	3.10%	0.00%	0.00%	NA
Intermediate	90	58.90%	23.30%	8.89%	8.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0801822513	C -> T	LOC_Os08g03810.1	synonymous_variant ; p.Ala25Ala; LOW	synonymous_codon	Average:59.082; most accessible tissue: Minghui63 flag leaf, score: 79.962	N	N	N	N
vg0801822513	C -> DEL	LOC_Os08g03810.1	N	frameshift_variant	Average:59.082; most accessible tissue: Minghui63 flag leaf, score: 79.962	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0801822513	6.96E-07	1.70E-11	mr1739	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
vg0801822513	7.08E-07	1.77E-16	mr1739	Ind_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
vg0801822513	NA	5.91E-07	mr1881	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
vg0801822513	NA	7.65E-10	mr1327_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
vg0801822513	NA	5.70E-17	mr1352_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
vg0801822513	NA	2.88E-06	mr1483_2	Ind_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
vg0801822513	NA	9.26E-07	mr1654_2	Ind_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
vg0801822513	NA	9.61E-12	mr1734_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
vg0801822513	1.11E-06	2.99E-11	mr1739_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
vg0801822513	4.18E-07	1.63E-16	mr1739_2	Ind_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
vg0801822513	NA	1.24E-13	mr1807_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
vg0801822513	NA	7.86E-07	mr1807_2	Ind_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