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Detailed information for vg1201807653:

Variant ID: vg1201807653 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 1807653
Reference Allele: G	Alternative Allele: C
Primary Allele: G	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGGTGAGTTTATGAGGTCTCTAAAGAATTCGTTACATTCCAAGAGCATTAATGCATCCACCGAAATGAATTATCCGTAGCAATTTTGGTCATCGTGTTTA[G/C]
CATCGACTTGTGCAGCCTGTGAATTGAAGTAGAAGGGCATATATATATATATATATATATTTCTCTGTTCTGCTCTTGCCTCTGTCTACAAAATTCCACG

Reverse complement sequence

CGTGGAATTTTGTAGACAGAGGCAAGAGCAGAACAGAGAAATATATATATATATATATATATGCCCTTCTACTTCAATTCACAGGCTGCACAAGTCGATG[C/G]
TAAACACGATGACCAAAATTGCTACGGATAATTCATTTCGGTGGATGCATTAATGCTCTTGGAATGTAACGAATTCTTTAGAGACCTCATAAACTCACCA

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	93.60%	3.20%	3.17%	0.00%	NA
All Indica	2759	89.20%	5.40%	5.36%	0.00%	NA
All Japonica	1512	99.90%	0.10%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	67.10%	17.30%	15.63%	0.00%	NA
Indica II	465	97.60%	0.60%	1.72%	0.00%	NA
Indica III	913	95.30%	2.60%	2.08%	0.00%	NA
Indica Intermediate	786	93.90%	2.50%	3.56%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	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	97.80%	0.00%	2.22%	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
vg1201807653	G -> C	LOC_Os12g04260.1	downstream_gene_variant ; 137.0bp to feature; MODIFIER	silent_mutation	Average:48.863; most accessible tissue: Zhenshan97 root, score: 66.982	N	N	N	N
vg1201807653	G -> C	LOC_Os12g04270.1	downstream_gene_variant ; 18.0bp to feature; MODIFIER	silent_mutation	Average:48.863; most accessible tissue: Zhenshan97 root, score: 66.982	N	N	N	N
vg1201807653	G -> C	LOC_Os12g04270.2	downstream_gene_variant ; 18.0bp to feature; MODIFIER	silent_mutation	Average:48.863; most accessible tissue: Zhenshan97 root, score: 66.982	N	N	N	N
vg1201807653	G -> C	LOC_Os12g04260-LOC_Os12g04270	intergenic_region ; MODIFIER	silent_mutation	Average:48.863; most accessible tissue: Zhenshan97 root, score: 66.982	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1201807653	NA	8.20E-06	mr1333	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
vg1201807653	NA	1.42E-06	mr1686	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