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Detailed information for vg0601347422:

Variant ID: vg0601347422 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 1347422
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 36. )

Flanking Sequence (100 bp) in Reference Genome:

ATGGACGGATTCCTTTGCTTCCTCTTCAACATTGGAGCCTTCGTCTTTCGTCAGGACTACAGGGAGCCCCAAGTCGATTTTGCTTCGGTCTTGAAGCAGC[C/T]
GCAATGCGGGTGTCTTGGGGTGCGCCTTTACTTCCTGTTCCAGCAGATCAAGCCCCGCCACATCACACCCAAGTGAAATCTCGTTGAGCTGTTCGAGGTG

Reverse complement sequence

CACCTCGAACAGCTCAACGAGATTTCACTTGGGTGTGATGTGGCGGGGCTTGATCTGCTGGAACAGGAAGTAAAGGCGCACCCCAAGACACCCGCATTGC[G/A]
GCTGCTTCAAGACCGAAGCAAAATCGACTTGGGGCTCCCTGTAGTCCTGACGAAAGACGAAGGCTCCAATGTTGAAGAGGAAGCAAAGGAATCCGTCCAT

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	67.40%	32.50%	0.13%	0.00%	NA
All Indica	2759	86.50%	13.40%	0.14%	0.00%	NA
All Japonica	1512	27.90%	72.10%	0.00%	0.00%	NA
Aus	269	99.30%	0.70%	0.00%	0.00%	NA
Indica I	595	95.50%	4.40%	0.17%	0.00%	NA
Indica II	465	58.50%	41.30%	0.22%	0.00%	NA
Indica III	913	96.90%	3.00%	0.11%	0.00%	NA
Indica Intermediate	786	84.10%	15.80%	0.13%	0.00%	NA
Temperate Japonica	767	14.90%	85.10%	0.00%	0.00%	NA
Tropical Japonica	504	49.20%	50.80%	0.00%	0.00%	NA
Japonica Intermediate	241	24.90%	75.10%	0.00%	0.00%	NA
VI/Aromatic	96	65.60%	34.40%	0.00%	0.00%	NA
Intermediate	90	50.00%	47.80%	2.22%	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
vg0601347422	C -> T	LOC_Os06g03500.1	missense_variant ; p.Arg961Gln; MODERATE	nonsynonymous_codon ; R961Q	Average:65.067; most accessible tissue: Minghui63 root, score: 79.068	unknown	unknown	TOLERATED	0.43

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0601347422	1.13E-06	2.58E-13	mr1141	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
vg0601347422	7.18E-06	1.76E-12	mr1141_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
vg0601347422	NA	2.57E-06	mr1561_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