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Detailed information for vg0611161418:

Variant ID: vg0611161418 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 11161418
Reference Allele: C	Alternative Allele: G
Primary Allele: G	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACCCGAATTCCTTCGAAGACTCCGAGAGCTGTTCTATTCTACTCCACTTAGCAATAGAATACTAAACTAAAGTATAAAGAGAAATGTTGAGCTTGCTTGA[C/G]
TGTAGGGGTGAAAACGGTAATGGTAATTACCGGCCGACCGGCGTTCGTTTCTAACTTTGTACCGGCCGAACCATATGGAAATGGTAATAGACTGAAAAAA

Reverse complement sequence

TTTTTTCAGTCTATTACCATTTCCATATGGTTCGGCCGGTACAAAGTTAGAAACGAACGCCGGTCGGCCGGTAATTACCATTACCGTTTTCACCCCTACA[G/C]
TCAAGCAAGCTCAACATTTCTCTTTATACTTTAGTTTAGTATTCTATTGCTAAGTGGAGTAGAATAGAACAGCTCTCGGAGTCTTCGAAGGAATTCGGGT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	92.70%	7.30%	0.00%	0.00%	NA
All Indica	2759	99.60%	0.40%	0.00%	0.00%	NA
All Japonica	1512	78.30%	21.70%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.70%	0.30%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	99.90%	0.10%	0.00%	0.00%	NA
Indica Intermediate	786	99.10%	0.90%	0.00%	0.00%	NA
Temperate Japonica	767	63.60%	36.40%	0.00%	0.00%	NA
Tropical Japonica	504	98.60%	1.40%	0.00%	0.00%	NA
Japonica Intermediate	241	82.60%	17.40%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	94.40%	5.60%	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
vg0611161418	C -> G	LOC_Os06g19580-LOC_Os06g19590	intergenic_region ; MODIFIER	silent_mutation	Average:32.969; most accessible tissue: Zhenshan97 young leaf, score: 45.281	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0611161418	3.30E-07	NA	mr1310	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
vg0611161418	NA	4.88E-07	mr1570	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
vg0611161418	1.62E-09	NA	mr1926	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
vg0611161418	NA	1.07E-07	mr1926	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
vg0611161418	NA	1.33E-06	mr1161_2	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