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Detailed information for vg0607338126:

Variant ID: vg0607338126 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 7338126
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.02, others allele: 0.00, population size: 55. )

Flanking Sequence (100 bp) in Reference Genome:

AGTCTAGTTTTAGTAAGACCAAGTAATTAAGGTTGTGCTCAGGCCGGTCGATGTCAATGCCATCATGCAAGAAAATGAAGGAGGAGGAGAGGCGCAAGCA[C/T]
GAGGTGGTGGCGCTGTATGAGCTAGGGCTTCGGCATGCTGGTGTTGGGGGTGGCACTGTTCGAGGGCTCCTTGCCGCAGGTCTCACACAAATAGTGATAC

Reverse complement sequence

GTATCACTATTTGTGTGAGACCTGCGGCAAGGAGCCCTCGAACAGTGCCACCCCCAACACCAGCATGCCGAAGCCCTAGCTCATACAGCGCCACCACCTC[G/A]
TGCTTGCGCCTCTCCTCCTCCTTCATTTTCTTGCATGATGGCATTGACATCGACCGGCCTGAGCACAACCTTAATTACTTGGTCTTACTAAAACTAGACT

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	51.30%	6.70%	12.87%	29.18%	NA
All Indica	2759	23.70%	10.90%	19.35%	46.03%	NA
All Japonica	1512	98.90%	0.10%	0.46%	0.60%	NA
Aus	269	68.40%	0.00%	1.12%	30.48%	NA
Indica I	595	28.70%	6.60%	18.15%	46.55%	NA
Indica II	465	12.70%	15.70%	20.22%	51.40%	NA
Indica III	913	24.50%	13.10%	20.81%	41.51%	NA
Indica Intermediate	786	25.40%	8.80%	18.07%	47.71%	NA
Temperate Japonica	767	99.30%	0.00%	0.13%	0.52%	NA
Tropical Japonica	504	99.20%	0.00%	0.00%	0.79%	NA
Japonica Intermediate	241	96.70%	0.40%	2.49%	0.41%	NA
VI/Aromatic	96	29.20%	12.50%	46.88%	11.46%	NA
Intermediate	90	68.90%	2.20%	21.11%	7.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0607338126	C -> T	LOC_Os06g13340.1	synonymous_variant ; p.His17His; LOW	synonymous_codon	Average:41.465; most accessible tissue: Minghui63 panicle, score: 59.629	N	N	N	N
vg0607338126	C -> DEL	LOC_Os06g13340.1	N	frameshift_variant	Average:41.465; most accessible tissue: Minghui63 panicle, score: 59.629	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0607338126	3.24E-06	3.24E-06	mr1643_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
vg0607338126	7.09E-06	7.09E-06	mr1643_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