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Detailed information for vg0727278538:

Variant ID: vg0727278538 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 27278538
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTAAAGACTTTTGTGAAGACTTCGGAATTAAGATTTGCTATGCTTCAGTGGCACACCCCATGAGCAATGGACAGGTGGAGCGAGCCAATGGCATGATACT[C/T]
CAAGGGATTAAAGCACGTGTTTTTGACCGGCTAAAACCCTATGCCGGCAAATGGGTGCAACAGCTGCCATCAGTACTTTGGTCTTTGCGAACTACACCCA

Reverse complement sequence

TGGGTGTAGTTCGCAAAGACCAAAGTACTGATGGCAGCTGTTGCACCCATTTGCCGGCATAGGGTTTTAGCCGGTCAAAAACACGTGCTTTAATCCCTTG[G/A]
AGTATCATGCCATTGGCTCGCTCCACCTGTCCATTGCTCATGGGGTGTGCCACTGAAGCATAGCAAATCTTAATTCCGAAGTCTTCACAAAAGTCTTTAA

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	47.20%	2.00%	18.66%	32.14%	NA
All Indica	2759	25.50%	3.30%	23.85%	47.37%	NA
All Japonica	1512	93.40%	0.10%	5.29%	1.19%	NA
Aus	269	14.50%	0.00%	19.33%	66.17%	NA
Indica I	595	38.30%	1.00%	10.42%	50.25%	NA
Indica II	465	28.00%	5.40%	18.92%	47.74%	NA
Indica III	913	7.30%	4.30%	38.01%	50.38%	NA
Indica Intermediate	786	35.40%	2.70%	20.48%	41.48%	NA
Temperate Japonica	767	96.50%	0.30%	1.96%	1.30%	NA
Tropical Japonica	504	87.50%	0.00%	11.51%	0.99%	NA
Japonica Intermediate	241	95.90%	0.00%	2.90%	1.24%	NA
VI/Aromatic	96	24.00%	0.00%	71.88%	4.17%	NA
Intermediate	90	61.10%	0.00%	25.56%	13.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0727278538	C -> DEL	LOC_Os07g45680.1	N	frameshift_variant	Average:14.205; most accessible tissue: Minghui63 panicle, score: 25.313	N	N	N	N
vg0727278538	C -> T	LOC_Os07g45680.1	synonymous_variant ; p.Leu1794Leu; LOW	synonymous_codon	Average:14.205; most accessible tissue: Minghui63 panicle, score: 25.313	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0727278538	4.98E-06	2.01E-06	mr1923	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
vg0727278538	NA	6.37E-07	mr1369_2	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
vg0727278538	NA	4.21E-07	mr1453_2	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