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Detailed information for vg1200352341:

Variant ID: vg1200352341 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 352341
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 259. )

Flanking Sequence (100 bp) in Reference Genome:

CCGTAAGCATATTACTTATTTATATGGATACCAGCATATTACAGAGCACAAAATATTTACCTAACGGGCCCTTGAAACTGATCACCCTAAAGGCATTAGC[C/T]
CATTAATAAAATTTTGGGGGACCAAATTTAGTCTGCAACACCTACTCTCCTTTGGTTTATTCATTTCAAACATAGTGAGCTTAAGGCTACGTAACCTTGG

Reverse complement sequence

CCAAGGTTACGTAGCCTTAAGCTCACTATGTTTGAAATGAATAAACCAAAGGAGAGTAGGTGTTGCAGACTAAATTTGGTCCCCCAAAATTTTATTAATG[G/A]
GCTAATGCCTTTAGGGTGATCAGTTTCAAGGGCCCGTTAGGTAAATATTTTGTGCTCTGTAATATGCTGGTATCCATATAAATAAGTAATATGCTTACGG

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	61.00%	38.70%	0.21%	0.11%	NA
All Indica	2759	36.00%	63.50%	0.33%	0.11%	NA
All Japonica	1512	96.40%	3.60%	0.00%	0.07%	NA
Aus	269	98.90%	0.70%	0.00%	0.37%	NA
Indica I	595	47.20%	52.60%	0.17%	0.00%	NA
Indica II	465	18.10%	81.10%	0.22%	0.65%	NA
Indica III	913	38.30%	61.60%	0.11%	0.00%	NA
Indica Intermediate	786	35.50%	63.70%	0.76%	0.00%	NA
Temperate Japonica	767	94.70%	5.30%	0.00%	0.00%	NA
Tropical Japonica	504	97.60%	2.20%	0.00%	0.20%	NA
Japonica Intermediate	241	99.20%	0.80%	0.00%	0.00%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	77.80%	21.10%	1.11%	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
vg1200352341	C -> DEL	N	N	silent_mutation	Average:55.577; most accessible tissue: Minghui63 flag leaf, score: 76.091	N	N	N	N
vg1200352341	C -> T	LOC_Os12g01574.1	upstream_gene_variant ; 1696.0bp to feature; MODIFIER	silent_mutation	Average:55.577; most accessible tissue: Minghui63 flag leaf, score: 76.091	N	N	N	N
vg1200352341	C -> T	LOC_Os12g01570.1	downstream_gene_variant ; 3196.0bp to feature; MODIFIER	silent_mutation	Average:55.577; most accessible tissue: Minghui63 flag leaf, score: 76.091	N	N	N	N
vg1200352341	C -> T	LOC_Os12g01590.1	downstream_gene_variant ; 3182.0bp to feature; MODIFIER	silent_mutation	Average:55.577; most accessible tissue: Minghui63 flag leaf, score: 76.091	N	N	N	N
vg1200352341	C -> T	LOC_Os12g01580.1	intron_variant ; MODIFIER	silent_mutation	Average:55.577; most accessible tissue: Minghui63 flag leaf, score: 76.091	N	N	N	N
vg1200352341	C -> T	LOC_Os12g01580.2	intron_variant ; MODIFIER	silent_mutation	Average:55.577; most accessible tissue: Minghui63 flag leaf, score: 76.091	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1200352341	NA	2.50E-08	mr1174	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