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Detailed information for vg0102531039:

Variant ID: vg0102531039 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 2531039
Reference Allele: C	Alternative Allele: A
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GTACCGAAGCATTTGAGATCAGGTGGTGATTAGTTCGGCCAGTACGTGAGCTGACTATGATGCAGGTCGGTAGAGACAATCTGGAGATGCTGCAGCAGGT[C/A]
GGTAGCTACAGTCTTGAGATCGGCGCCGCCGAAGCCGCCGGAGTCGCTGGCGAAGAGTACCGCTCCGGCACGCCGCCGCCGGGGCAGTTCGTGAAGGAGC

Reverse complement sequence

GCTCCTTCACGAACTGCCCCGGCGGCGGCGTGCCGGAGCGGTACTCTTCGCCAGCGACTCCGGCGGCTTCGGCGGCGCCGATCTCAAGACTGTAGCTACC[G/T]
ACCTGCTGCAGCATCTCCAGATTGTCTCTACCGACCTGCATCATAGTCAGCTCACGTACTGGCCGAACTAATCACCACCTGATCTCAAATGCTTCGGTAC

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	50.80%	47.90%	0.66%	0.70%	NA
All Indica	2759	70.20%	29.20%	0.36%	0.18%	NA
All Japonica	1512	16.70%	82.20%	1.12%	0.00%	NA
Aus	269	62.10%	27.10%	0.37%	10.41%	NA
Indica I	595	90.90%	8.70%	0.34%	0.00%	NA
Indica II	465	66.70%	32.90%	0.22%	0.22%	NA
Indica III	913	59.60%	39.80%	0.33%	0.33%	NA
Indica Intermediate	786	69.00%	30.40%	0.51%	0.13%	NA
Temperate Japonica	767	13.70%	84.50%	1.83%	0.00%	NA
Tropical Japonica	504	20.60%	79.20%	0.20%	0.00%	NA
Japonica Intermediate	241	17.80%	81.30%	0.83%	0.00%	NA
VI/Aromatic	96	18.80%	81.20%	0.00%	0.00%	NA
Intermediate	90	27.80%	68.90%	3.33%	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
vg0102531039	C -> A	LOC_Os01g05350.1	synonymous_variant ; p.Val106Val; LOW	synonymous_codon	Average:72.196; most accessible tissue: Callus, score: 87.858	N	N	N	N
vg0102531039	C -> DEL	LOC_Os01g05350.1	N	frameshift_variant	Average:72.196; most accessible tissue: Callus, score: 87.858	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0102531039	NA	2.94E-06	mr1119	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
vg0102531039	NA	6.40E-06	mr1123	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
vg0102531039	2.16E-06	1.26E-07	mr1242	Jap_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
vg0102531039	8.60E-06	8.60E-06	mr1529	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
vg0102531039	1.22E-06	1.22E-06	mr1967	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