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Detailed information for vg0712050315:

Variant ID: vg0712050315 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 12050315
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TACATACCACTAGGGGAAAATCAATGAAAACTAAAGTATGAAAGTCGCCGTCGTATATGGGATGAGCCATACCTATATCGGGTCTACTCCGATGGCTTAC[T/C]
ACGAAGATGTGTGCCAATTGATGAAGGACTTAGGATCATAGAGAAATGCCATGCCTCACCCTATGATGGCCATTACGGTGCATTCCACACTCAGGCCAAG

Reverse complement sequence

CTTGGCCTGAGTGTGGAATGCACCGTAATGGCCATCATAGGGTGAGGCATGGCATTTCTCTATGATCCTAAGTCCTTCATCAATTGGCACACATCTTCGT[A/G]
GTAAGCCATCGGAGTAGACCCGATATAGGTATGGCTCATCCCATATACGACGGCGACTTTCATACTTTAGTTTTCATTGATTTTCCCCTAGTGGTATGTA

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	55.40%	18.30%	5.08%	21.16%	NA
All Indica	2759	81.40%	4.40%	6.13%	8.08%	NA
All Japonica	1512	10.00%	44.00%	2.98%	42.99%	NA
Aus	269	53.90%	19.30%	3.72%	23.05%	NA
Indica I	595	69.10%	0.80%	10.08%	20.00%	NA
Indica II	465	87.70%	6.50%	4.30%	1.51%	NA
Indica III	913	93.10%	3.00%	2.52%	1.42%	NA
Indica Intermediate	786	73.40%	7.50%	8.40%	10.69%	NA
Temperate Japonica	767	5.30%	57.40%	1.96%	35.33%	NA
Tropical Japonica	504	17.30%	28.20%	4.17%	50.40%	NA
Japonica Intermediate	241	9.50%	34.90%	3.73%	51.87%	NA
VI/Aromatic	96	25.00%	7.30%	11.46%	56.25%	NA
Intermediate	90	58.90%	23.30%	5.56%	12.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0712050315	T -> DEL	N	N	silent_mutation	Average:26.38; most accessible tissue: Zhenshan97 panicle, score: 46.362	N	N	N	N
vg0712050315	T -> C	LOC_Os07g20840.1	downstream_gene_variant ; 3665.0bp to feature; MODIFIER	silent_mutation	Average:26.38; most accessible tissue: Zhenshan97 panicle, score: 46.362	N	N	N	N
vg0712050315	T -> C	LOC_Os07g20830.1	intron_variant ; MODIFIER	silent_mutation	Average:26.38; most accessible tissue: Zhenshan97 panicle, score: 46.362	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0712050315	NA	6.10E-07	mr1915	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
vg0712050315	5.94E-06	NA	mr1950	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
vg0712050315	NA	1.03E-06	mr1950	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
vg0712050315	NA	1.83E-07	mr1855_2	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