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Detailed information for vg0107832208:

Variant ID: vg0107832208 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 7832208
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 126. )

Flanking Sequence (100 bp) in Reference Genome:

ATGTGTGAGACGTGGAGGTCGGAGTCTGGATACGCTGAGTCCGGTTCGTGAGGAGCCGTCTCTTCGTTCGTCTCGACAACGCGTACTCGCTTGCCTTTTT[C/T]
AAATGCCATGTGCTTCTCGAGCGACTTTTTGAAAACAAGGCAATCTTCCAGAGAATGTCTGTCCGTCTTGTGTATGGAGCACCATGATTTCTTTATGTCG

Reverse complement sequence

CGACATAAAGAAATCATGGTGCTCCATACACAAGACGGACAGACATTCTCTGGAAGATTGCCTTGTTTTCAAAAAGTCGCTCGAGAAGCACATGGCATTT[G/A]
AAAAAGGCAAGCGAGTACGCGTTGTCGAGACGAACGAAGAGACGGCTCCTCACGAACCGGACTCAGCGTATCCAGACTCCGACCTCCACGTCTCACACAT

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	44.10%	7.30%	46.04%	2.52%	NA
All Indica	2759	8.60%	12.50%	74.66%	4.28%	NA
All Japonica	1512	97.10%	0.10%	2.71%	0.07%	NA
Aus	269	87.70%	0.00%	12.27%	0.00%	NA
Indica I	595	5.50%	6.90%	78.82%	8.74%	NA
Indica II	465	6.00%	9.70%	77.85%	6.45%	NA
Indica III	913	10.60%	18.90%	70.10%	0.33%	NA
Indica Intermediate	786	10.10%	10.80%	74.94%	4.20%	NA
Temperate Japonica	767	97.90%	0.10%	1.96%	0.00%	NA
Tropical Japonica	504	95.40%	0.20%	4.37%	0.00%	NA
Japonica Intermediate	241	97.90%	0.00%	1.66%	0.41%	NA
VI/Aromatic	96	97.90%	0.00%	2.08%	0.00%	NA
Intermediate	90	54.40%	1.10%	44.44%	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
vg0107832208	C -> T	LOC_Os01g13970.1	missense_variant ; p.Glu4Lys; MODERATE	nonsynonymous_codon ; E4K	Average:25.778; most accessible tissue: Minghui63 root, score: 41.911	benign	0.917	TOLERATED	0.06
vg0107832208	C -> DEL	LOC_Os01g13970.1	N	frameshift_variant	Average:25.778; most accessible tissue: Minghui63 root, score: 41.911	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0107832208	2.33E-06	NA	mr1037_2	Ind_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