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Detailed information for vg0138577662:

Variant ID: vg0138577662 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 38577662
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCGCCTCATCCATTCATCTGCTGGCAAGTGGCAACCCGCTGCGCCGCCGTGCGTGCGCGCAGGAGTCGCCGAGGAGTTGGAGGATCTCGATCGACGAAGT[T/C]
GCCGTCGTCGCCGACAGCGACGGCGATGCAGATGTCAACGCTGAGCAGCTCCTCCATTTGCTCGAGCACGTCGGCGCCATAGGGGAGAACACGTACGGTT

Reverse complement sequence

AACCGTACGTGTTCTCCCCTATGGCGCCGACGTGCTCGAGCAAATGGAGGAGCTGCTCAGCGTTGACATCTGCATCGCCGTCGCTGTCGGCGACGACGGC[A/G]
ACTTCGTCGATCGAGATCCTCCAACTCCTCGGCGACTCCTGCGCGCACGCACGGCGGCGCAGCGGGTTGCCACTTGCCAGCAGATGAATGGATGAGGCGA

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	87.50%	9.90%	2.67%	0.00%	NA
All Indica	2759	99.90%	0.00%	0.04%	0.00%	NA
All Japonica	1512	61.20%	30.60%	8.20%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.80%	0.20%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.90%	0.00%	0.13%	0.00%	NA
Temperate Japonica	767	62.50%	24.00%	13.56%	0.00%	NA
Tropical Japonica	504	73.40%	24.80%	1.79%	0.00%	NA
Japonica Intermediate	241	32.00%	63.50%	4.56%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	95.60%	3.30%	1.11%	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
vg0138577662	T -> C	LOC_Os01g66440.1	synonymous_variant ; p.Val167Val; LOW	synonymous_codon	Average:77.426; most accessible tissue: Minghui63 root, score: 87.285	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0138577662	7.09E-06	NA	mr1064_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
vg0138577662	NA	6.58E-09	mr1691_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