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Detailed information for vg0714044539:

Variant ID: vg0714044539 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 14044539
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CAATCTATCTATGGAACAACATATGACAGACATTTGTATGCTTAAACCAAAAGAAGAAGTTCCAGTGGTGCAAGAATATTTCGATGTATTTCCTGAAGAA[C/T]
TAAGTTCATTACCTCCAGATCGGGAAATAGAATTTATTATAGAATTACTTCCTGGAATGGCACCTATATCAAAAAGACCCTATAGGATGCCAATTAATGA

Reverse complement sequence

TCATTAATTGGCATCCTATAGGGTCTTTTTGATATAGGTGCCATTCCAGGAAGTAATTCTATAATAAATTCTATTTCCCGATCTGGAGGTAATGAACTTA[G/A]
TTCTTCAGGAAATACATCGAAATATTCTTGCACCACTGGAACTTCTTCTTTTGGTTTAAGCATACAAATGTCTGTCATATGTTGTTCCATAGATAGATTG

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	44.00%	0.10%	1.12%	54.72%	NA
All Indica	2759	23.80%	0.20%	1.49%	74.48%	NA
All Japonica	1512	81.30%	0.10%	0.13%	18.45%	NA
Aus	269	23.00%	0.00%	3.35%	73.61%	NA
Indica I	595	46.60%	0.20%	1.51%	51.76%	NA
Indica II	465	26.70%	0.40%	4.09%	68.82%	NA
Indica III	913	3.20%	0.10%	0.11%	96.60%	NA
Indica Intermediate	786	28.90%	0.30%	1.53%	69.34%	NA
Temperate Japonica	767	81.20%	0.10%	0.26%	18.38%	NA
Tropical Japonica	504	92.50%	0.00%	0.00%	7.54%	NA
Japonica Intermediate	241	58.50%	0.00%	0.00%	41.49%	NA
VI/Aromatic	96	82.30%	0.00%	0.00%	17.71%	NA
Intermediate	90	57.80%	0.00%	1.11%	41.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0714044539	C -> DEL	LOC_Os07g24690.1	N	frameshift_variant	Average:10.435; most accessible tissue: Callus, score: 35.62	N	N	N	N
vg0714044539	C -> T	LOC_Os07g24690.1	synonymous_variant ; p.Leu158Leu; LOW	synonymous_codon	Average:10.435; most accessible tissue: Callus, score: 35.62	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0714044539	NA	1.33E-13	mr1170	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
vg0714044539	4.52E-06	4.52E-06	mr1569	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
vg0714044539	NA	6.06E-11	mr1713	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
vg0714044539	NA	2.83E-11	mr1905	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