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Detailed information for vg0611642002:

Variant ID: vg0611642002 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 11642002
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GGGGTCTAGCCAGTGGCAACGAAGGTTGGTTGCCTGCTACTCCTAGTGGCAGCCGCGACCACAGCAGCAGCAGTTCCAGTGGCTCAGAGCCGGGCAACGG[C/T]
GAGACGTATCTGCCAGACTCCAGGAGCCGCTCAGAGGGACCTGGCGACGAGCAGGAGGACGCCTTCAACTCCACCGACCGCAGGAGCCGTTCCGAGCATT

Reverse complement sequence

AATGCTCGGAACGGCTCCTGCGGTCGGTGGAGTTGAAGGCGTCCTCCTGCTCGTCGCCAGGTCCCTCTGAGCGGCTCCTGGAGTCTGGCAGATACGTCTC[G/A]
CCGTTGCCCGGCTCTGAGCCACTGGAACTGCTGCTGCTGTGGTCGCGGCTGCCACTAGGAGTAGCAGGCAACCAACCTTCGTTGCCACTGGCTAGACCCC

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	96.60%	3.00%	0.38%	0.00%	NA
All Indica	2759	94.30%	5.10%	0.62%	0.00%	NA
All Japonica	1512	99.90%	0.00%	0.07%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	95.60%	4.40%	0.00%	0.00%	NA
Indica II	465	93.80%	6.00%	0.22%	0.00%	NA
Indica III	913	92.80%	5.80%	1.42%	0.00%	NA
Indica Intermediate	786	95.40%	4.20%	0.38%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.00%	0.20%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	100.00%	0.00%	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
vg0611642002	C -> T	LOC_Os06g20280.1	synonymous_variant ; p.Ser74Ser; LOW	synonymous_codon	Average:65.916; most accessible tissue: Minghui63 young leaf, score: 76.82	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0611642002	1.34E-10	5.26E-15	mr1695	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
vg0611642002	8.49E-06	NA	mr1091_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
vg0611642002	4.41E-10	1.90E-11	mr1695_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