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Detailed information for vg1206433470:

Variant ID: vg1206433470 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 6433470
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTCGGAAGGAATTTTGATGTAGGACCAAATCCATTGGAAAGGTGGTCTCGTTAGCTTTCCATGCATATGTAGAACATCGAAATCGGAGTCAGAATACAAC[C/T]
TGGGCGATGAATTTAGTGTGTAATACTCCTGGAGCCTGAAGTGGACTTAAACTTGATATGAGTTGGATCTCCATCTTGACTTGAACGCTCATGATGACTT

Reverse complement sequence

AAGTCATCATGAGCGTTCAAGTCAAGATGGAGATCCAACTCATATCAAGTTTAAGTCCACTTCAGGCTCCAGGAGTATTACACACTAAATTCATCGCCCA[G/A]
GTTGTATTCTGACTCCGATTTCGATGTTCTACATATGCATGGAAAGCTAACGAGACCACCTTTCCAATGGATTTGGTCCTACATCAAAATTCCTTCCGAA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	25.20%	16.50%	0.34%	57.96%	NA
All Indica	2759	36.50%	7.80%	0.36%	55.27%	NA
All Japonica	1512	5.60%	31.30%	0.33%	62.76%	NA
Aus	269	1.50%	22.30%	0.37%	75.84%	NA
Indica I	595	86.60%	4.40%	0.17%	8.91%	NA
Indica II	465	20.40%	18.70%	0.43%	60.43%	NA
Indica III	913	11.20%	3.60%	0.44%	84.78%	NA
Indica Intermediate	786	37.70%	8.90%	0.38%	53.05%	NA
Temperate Japonica	767	8.50%	41.10%	0.65%	49.80%	NA
Tropical Japonica	504	2.40%	10.70%	0.00%	86.90%	NA
Japonica Intermediate	241	2.90%	43.60%	0.00%	53.53%	NA
VI/Aromatic	96	69.80%	10.40%	0.00%	19.79%	NA
Intermediate	90	30.00%	23.30%	0.00%	46.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1206433470	C -> DEL	N	N	silent_mutation	Average:60.017; most accessible tissue: Minghui63 flag leaf, score: 74.955	N	N	N	N
vg1206433470	C -> T	LOC_Os12g11840.1	downstream_gene_variant ; 3678.0bp to feature; MODIFIER	silent_mutation	Average:60.017; most accessible tissue: Minghui63 flag leaf, score: 74.955	N	N	N	N
vg1206433470	C -> T	LOC_Os12g11840-LOC_Os12g11860	intergenic_region ; MODIFIER	silent_mutation	Average:60.017; most accessible tissue: Minghui63 flag leaf, score: 74.955	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1206433470	1.47E-06	1.47E-06	mr1173	Jap_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
vg1206433470	1.19E-07	1.19E-07	mr1381	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