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Detailed information for vg0801228810:

Variant ID: vg0801228810 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 1228810
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TACAAAAGATACAATAGAGCCTCTTGTAATTCAGCTCAAAGTTGTGTGTTGGAAATGAGAGTGAGCTCCTCCTTTTATAGGCAGGTATGACGGTTACAGC[C/A]
TATGCGAAATGACCAAACTACCCTGGAACCGCCATTAGGATGTGATCAGGGCCGTCCATGCAAAATTTGACGATCAACGGCCAGCAAAACGGTTCGTCCG

Reverse complement sequence

CGGACGAACCGTTTTGCTGGCCGTTGATCGTCAAATTTTGCATGGACGGCCCTGATCACATCCTAATGGCGGTTCCAGGGTAGTTTGGTCATTTCGCATA[G/T]
GCTGTAACCGTCATACCTGCCTATAAAAGGAGGAGCTCACTCTCATTTCCAACACACAACTTTGAGCTGAATTACAAGAGGCTCTATTGTATCTTTTGTA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	93.00%	6.50%	0.19%	0.25%	NA
All Indica	2759	96.50%	2.80%	0.29%	0.43%	NA
All Japonica	1512	99.90%	0.10%	0.00%	0.00%	NA
Aus	269	17.50%	82.20%	0.37%	0.00%	NA
Indica I	595	99.30%	0.20%	0.17%	0.34%	NA
Indica II	465	99.40%	0.60%	0.00%	0.00%	NA
Indica III	913	95.70%	3.30%	0.00%	0.99%	NA
Indica Intermediate	786	93.60%	5.30%	0.89%	0.13%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	90.00%	10.00%	0.00%	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
vg0801228810	C -> A	LOC_Os08g02880.1	downstream_gene_variant ; 1284.0bp to feature; MODIFIER	silent_mutation	Average:46.972; most accessible tissue: Minghui63 panicle, score: 66.554	N	N	N	N
vg0801228810	C -> A	LOC_Os08g02870-LOC_Os08g02880	intergenic_region ; MODIFIER	silent_mutation	Average:46.972; most accessible tissue: Minghui63 panicle, score: 66.554	N	N	N	N
vg0801228810	C -> DEL	N	N	silent_mutation	Average:46.972; most accessible tissue: Minghui63 panicle, score: 66.554	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0801228810	7.21E-07	NA	mr1114	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
vg0801228810	1.49E-06	NA	mr1117	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
vg0801228810	2.19E-07	NA	mr1119	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
vg0801228810	5.17E-08	NA	mr1123	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
vg0801228810	2.48E-07	NA	mr1242	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
vg0801228810	2.77E-06	NA	mr1495	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
vg0801228810	2.48E-07	NA	mr1496	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
vg0801228810	NA	4.19E-07	mr1530	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
vg0801228810	NA	1.55E-07	mr1587	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
vg0801228810	NA	2.66E-07	mr1803	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
vg0801228810	1.40E-06	NA	mr1123_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
vg0801228810	2.62E-06	NA	mr1242_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
vg0801228810	1.72E-06	NA	mr1247_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
vg0801228810	2.29E-06	NA	mr1496_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
vg0801228810	NA	2.04E-16	mr1587_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
vg0801228810	NA	1.30E-12	mr1803_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