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Detailed information for vg0508129211:

Variant ID: vg0508129211 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 8129211
Reference Allele: G	Alternative Allele: C
Primary Allele: G	Secondary Allele: C

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.86, C: 0.14, others allele: 0.00, population size: 85. )

Flanking Sequence (100 bp) in Reference Genome:

TATTGGTTGTAATCTTCGACATCATCAACCCCATCCACTCCCAATATCTTTTGTTTCCCTGGTAGCACTATATCTTTCTTCAAATTTGAAGGGCCTTTCA[G/C]
ATAAAACACTTGTGCCACGCGATTGGCGAGTACCCAAGGGTCATCCTTGTGACCCACACTCGCAAGGTCAACAACAGTATGACCGAACTTATCAACATTG

Reverse complement sequence

CAATGTTGATAAGTTCGGTCATACTGTTGTTGACCTTGCGAGTGTGGGTCACAAGGATGACCCTTGGGTACTCGCCAATCGCGTGGCACAAGTGTTTTAT[C/G]
TGAAAGGCCCTTCAAATTTGAAGAAAGATATAGTGCTACCAGGGAAACAAAAGATATTGGGAGTGGATGGGGTTGATGATGTCGAAGATTACAACCAATA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	54.40%	1.70%	19.26%	24.69%	NA
All Indica	2759	31.00%	2.80%	26.10%	40.20%	NA
All Japonica	1512	98.90%	0.00%	0.33%	0.73%	NA
Aus	269	21.90%	0.70%	64.68%	12.64%	NA
Indica I	595	36.10%	3.40%	12.77%	47.73%	NA
Indica II	465	31.60%	4.10%	27.10%	37.20%	NA
Indica III	913	28.50%	1.00%	35.05%	35.49%	NA
Indica Intermediate	786	29.50%	3.60%	25.19%	41.73%	NA
Temperate Japonica	767	99.60%	0.00%	0.13%	0.26%	NA
Tropical Japonica	504	97.80%	0.00%	0.60%	1.59%	NA
Japonica Intermediate	241	99.20%	0.00%	0.41%	0.41%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	72.20%	1.10%	12.22%	14.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0508129211	G -> DEL	LOC_Os05g14420.1	N	frameshift_variant	Average:16.314; most accessible tissue: Callus, score: 28.203	N	N	N	N
vg0508129211	G -> C	LOC_Os05g14420.1	missense_variant ; p.Leu746Val; MODERATE	nonsynonymous_codon ; L746V	Average:16.314; most accessible tissue: Callus, score: 28.203	benign	-0.9	TOLERATED	1.00

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0508129211	1.85E-07	NA	mr1039_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
vg0508129211	8.71E-06	NA	mr1039_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