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Detailed information for vg0602861181:

Variant ID: vg0602861181 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 2861181
Reference Allele: C	Alternative Allele: G
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, G: 0.01, others allele: 0.00, population size: 295. )

Flanking Sequence (100 bp) in Reference Genome:

TTCTCCTCCGAAGCGAAGCGGACATCCCGATTTTCCATTGAGAAGTAATCGTTGTCTTCATCTGAAGATTCATCATCATCATCATCATATTCGGTTTCGT[C/G]
TGAATAATCGTCTTCCTCTCCATCTCCTGCTTCCTCCCATTCAGATTCTTTCTTCACCCATGAATCCACCTCATTGTCATCCTCTATCGAACAGAAAAAA

Reverse complement sequence

TTTTTTCTGTTCGATAGAGGATGACAATGAGGTGGATTCATGGGTGAAGAAAGAATCTGAATGGGAGGAAGCAGGAGATGGAGAGGAAGACGATTATTCA[G/C]
ACGAAACCGAATATGATGATGATGATGATGAATCTTCAGATGAAGACAACGATTACTTCTCAATGGAAAATCGGGATGTCCGCTTCGCTTCGGAGGAGAA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	93.20%	6.80%	0.04%	0.00%	NA
All Indica	2759	92.40%	7.50%	0.07%	0.00%	NA
All Japonica	1512	99.90%	0.10%	0.00%	0.00%	NA
Aus	269	60.60%	39.40%	0.00%	0.00%	NA
Indica I	595	86.70%	13.10%	0.17%	0.00%	NA
Indica II	465	99.80%	0.20%	0.00%	0.00%	NA
Indica III	913	98.70%	1.30%	0.00%	0.00%	NA
Indica Intermediate	786	85.10%	14.80%	0.13%	0.00%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	96.70%	3.30%	0.00%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0602861181	C -> G	LOC_Os06g06170.1	missense_variant ; p.Asp36His; MODERATE	nonsynonymous_codon ; D36H	Average:59.006; most accessible tissue: Minghui63 flag leaf, score: 76.807	unknown	unknown	TOLERATED	0.13

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0602861181	1.06E-06	2.81E-08	mr1477_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
vg0602861181	NA	1.09E-07	mr1971_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