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Detailed information for vg0505805966:

Variant ID: vg0505805966 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 5805966
Reference Allele: A	Alternative Allele: C
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TATAAAATTTGATTTCAAACTAATTCAAAACGTCAGGAATTATAAATCAGAGGAGTACTTTTTAAAAATGAAACTTGACATGATTATTTCCTTGTGTAAC[A/C]
CAAAGTAGTCCTAAATTTAAAAAAGAAAAAGAAAAAAAAATTATATTCATATTTCCGAGTATGCTTTTGTAAAAAAAACTATTTTTAAAGGAAATTATCA

Reverse complement sequence

TGATAATTTCCTTTAAAAATAGTTTTTTTTACAAAAGCATACTCGGAAATATGAATATAATTTTTTTTTCTTTTTCTTTTTTAAATTTAGGACTACTTTG[T/G]
GTTACACAAGGAAATAATCATGTCAAGTTTCATTTTTAAAAAGTACTCCTCTGATTTATAATTCCTGACGTTTTGAATTAGTTTGAAATCAAATTTTATA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	79.90%	19.70%	0.38%	0.00%	NA
All Indica	2759	89.70%	9.80%	0.47%	0.00%	NA
All Japonica	1512	63.50%	36.20%	0.33%	0.00%	NA
Aus	269	92.90%	7.10%	0.00%	0.00%	NA
Indica I	595	82.90%	16.10%	1.01%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	91.10%	8.70%	0.22%	0.00%	NA
Indica Intermediate	786	87.30%	12.10%	0.64%	0.00%	NA
Temperate Japonica	767	45.80%	53.60%	0.65%	0.00%	NA
Tropical Japonica	504	90.30%	9.70%	0.00%	0.00%	NA
Japonica Intermediate	241	63.90%	36.10%	0.00%	0.00%	NA
VI/Aromatic	96	20.80%	79.20%	0.00%	0.00%	NA
Intermediate	90	76.70%	23.30%	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
vg0505805966	A -> C	LOC_Os05g10640-LOC_Os05g10650	intergenic_region ; MODIFIER	silent_mutation	Average:33.427; most accessible tissue: Minghui63 root, score: 66.549	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0505805966	NA	7.44E-06	mr1672_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
vg0505805966	5.86E-06	2.24E-09	mr1793_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