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Detailed information for vg0714392517:

Variant ID: vg0714392517 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 14392517
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGTGTCCTAAGCCTCGGCGTGTGAAGAACGCTCCAGCCCCGAACAACTCTAATACTCCAGCACCGAAGGCACGTGTTAATCATGTTGTAGCGGCAGAAGC[T/C]
CAGAATGCACCAGATGTGGTTTTGGGTACGTTTCCTGTTAATTCTATACCCGCATCTGTGCTTTTTGATTCCGGTGCTACACATTCCTTTTTGTCTAAAA

Reverse complement sequence

TTTTAGACAAAAAGGAATGTGTAGCACCGGAATCAAAAAGCACAGATGCGGGTATAGAATTAACAGGAAACGTACCCAAAACCACATCTGGTGCATTCTG[A/G]
GCTTCTGCCGCTACAACATGATTAACACGTGCCTTCGGTGCTGGAGTATTAGAGTTGTTCGGGGCTGGAGCGTTCTTCACACGCCGAGGCTTAGGACACT

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	47.80%	0.50%	38.76%	12.99%	NA
All Indica	2759	28.30%	0.70%	53.61%	17.36%	NA
All Japonica	1512	83.90%	0.10%	8.93%	7.08%	NA
Aus	269	25.70%	0.70%	66.54%	7.06%	NA
Indica I	595	56.50%	0.70%	23.19%	19.66%	NA
Indica II	465	34.20%	0.40%	47.96%	17.42%	NA
Indica III	913	3.40%	0.70%	77.22%	18.73%	NA
Indica Intermediate	786	32.60%	0.90%	52.54%	13.99%	NA
Temperate Japonica	767	84.90%	0.00%	8.60%	6.52%	NA
Tropical Japonica	504	93.70%	0.00%	3.57%	2.78%	NA
Japonica Intermediate	241	60.20%	0.80%	21.16%	17.84%	NA
VI/Aromatic	96	83.30%	0.00%	15.62%	1.04%	NA
Intermediate	90	64.40%	0.00%	26.67%	8.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0714392517	T -> DEL	LOC_Os07g25190.1	N	frameshift_variant	Average:37.687; most accessible tissue: Zhenshan97 young leaf, score: 67.334	N	N	N	N
vg0714392517	T -> C	LOC_Os07g25190.1	synonymous_variant ; p.Ala502Ala; LOW	synonymous_codon	Average:37.687; most accessible tissue: Zhenshan97 young leaf, score: 67.334	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0714392517	4.99E-06	NA	mr1754	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