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Detailed information for vg0508125097:

Variant ID: vg0508125097 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 8125097
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.60, C: 0.40, others allele: 0.00, population size: 90. )

Flanking Sequence (100 bp) in Reference Genome:

AAGTTATGTAACCTTCTCATCTCCCATGGTGCTTCTTCTAGTGCCCATTCCGGCAACAGTGCTTTCCCATGTTCATACTTTTCCGGGCAATCATCGGTTG[T/C]
GAAGTATGTTGGCCCGGCTAGTTCAGCAGCCTTCTGGGGGTCGTCATCTCTGAGCTTGGCACGTTCCTTACCCCCTCTGAAGACGGTTACCATGAACTTC

Reverse complement sequence

GAAGTTCATGGTAACCGTCTTCAGAGGGGGTAAGGAACGTGCCAAGCTCAGAGATGACGACCCCCAGAAGGCTGCTGAACTAGCCGGGCCAACATACTTC[A/G]
CAACCGATGATTGCCCGGAAAAGTATGAACATGGGAAAGCACTGTTGCCGGAATGGGCACTAGAAGAAGCACCATGGGAGATGAGAAGGTTACATAACTT

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	69.30%	3.60%	14.64%	12.44%	NA
All Indica	2759	48.60%	6.10%	24.25%	20.99%	NA
All Japonica	1512	99.30%	0.00%	0.60%	0.13%	NA
Aus	269	96.70%	0.00%	2.60%	0.74%	NA
Indica I	595	40.30%	5.70%	25.38%	28.57%	NA
Indica II	465	37.00%	14.80%	27.74%	20.43%	NA
Indica III	913	57.50%	4.20%	23.55%	14.79%	NA
Indica Intermediate	786	51.50%	3.60%	22.14%	22.77%	NA
Temperate Japonica	767	99.60%	0.00%	0.13%	0.26%	NA
Tropical Japonica	504	98.60%	0.00%	1.39%	0.00%	NA
Japonica Intermediate	241	99.60%	0.00%	0.41%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	84.40%	2.20%	7.78%	5.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0508125097	T -> DEL	LOC_Os05g14410.1	N	frameshift_variant	Average:21.862; most accessible tissue: Minghui63 root, score: 33.152	N	N	N	N
vg0508125097	T -> C	LOC_Os05g14410.1	missense_variant ; p.Thr627Ala; MODERATE	nonsynonymous_codon ; T627A	Average:21.862; most accessible tissue: Minghui63 root, score: 33.152	benign	-0.381	TOLERATED	1.00

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0508125097	2.06E-06	NA	mr1834_2	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
vg0508125097	7.22E-07	1.99E-06	mr1834_2	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