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Detailed information for vg0607755407:

Variant ID: vg0607755407 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 7755407
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 92. )

Flanking Sequence (100 bp) in Reference Genome:

CTCTCTATCTCGGATGAGGAGCGGCGAGTTGGTGGCCGGCGATGGACGTGGCGGGGGTACGGGCGTGGTAGAGAGGCGGCCGGTGGCCGGAAAGCCACTG[C/T]
GGGCGGCGGGCGCTGTCGCCCTCGCGCACCGCCGGGAGCAGCAGCACGGTCGTCACCAGGGCGGCGTTAGCGGCGTCATCGTCGTCCACCTCCTTGCACC

Reverse complement sequence

GGTGCAAGGAGGTGGACGACGATGACGCCGCTAACGCCGCCCTGGTGACGACCGTGCTGCTGCTCCCGGCGGTGCGCGAGGGCGACAGCGCCCGCCGCCC[G/A]
CAGTGGCTTTCCGGCCACCGGCCGCCTCTCTACCACGCCCGTACCCCCGCCACGTCCATCGCCGGCCACCAACTCGCCGCTCCTCATCCGAGATAGAGAG

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	72.60%	22.90%	2.98%	1.54%	NA
All Indica	2759	56.30%	38.80%	4.93%	0.04%	NA
All Japonica	1512	99.60%	0.20%	0.00%	0.20%	NA
Aus	269	99.30%	0.40%	0.00%	0.37%	NA
Indica I	595	26.10%	62.50%	11.43%	0.00%	NA
Indica II	465	91.40%	3.90%	4.73%	0.00%	NA
Indica III	913	53.10%	45.80%	0.99%	0.11%	NA
Indica Intermediate	786	62.00%	33.30%	4.71%	0.00%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	97.90%	0.80%	0.00%	1.24%	NA
VI/Aromatic	96	28.10%	1.00%	3.12%	67.71%	NA
Intermediate	90	88.90%	5.60%	2.22%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0607755407	C -> T	LOC_Os06g13920.1	downstream_gene_variant ; 2352.0bp to feature; MODIFIER	silent_mutation	Average:64.82; most accessible tissue: Zhenshan97 young leaf, score: 76.44	N	N	N	N
vg0607755407	C -> T	LOC_Os06g13910-LOC_Os06g13920	intergenic_region ; MODIFIER	silent_mutation	Average:64.82; most accessible tissue: Zhenshan97 young leaf, score: 76.44	N	N	N	N
vg0607755407	C -> DEL	N	N	silent_mutation	Average:64.82; most accessible tissue: Zhenshan97 young leaf, score: 76.44	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0607755407	NA	8.83E-06	mr1158_2	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
vg0607755407	4.71E-07	NA	mr1184_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
vg0607755407	2.13E-06	2.64E-08	mr1184_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
vg0607755407	4.26E-06	NA	mr1278_2	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
vg0607755407	NA	5.96E-07	mr1278_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
vg0607755407	NA	1.07E-06	mr1332_2	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
vg0607755407	NA	9.93E-06	mr1332_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
vg0607755407	NA	6.66E-07	mr1371_2	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
vg0607755407	6.92E-06	9.74E-06	mr1373_2	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
vg0607755407	1.81E-06	1.81E-06	mr1374_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
vg0607755407	NA	7.97E-06	mr1417_2	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
vg0607755407	1.72E-06	2.36E-06	mr1633_2	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
vg0607755407	8.24E-06	6.49E-07	mr1633_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
vg0607755407	NA	2.34E-07	mr1641_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
vg0607755407	NA	1.78E-06	mr1648_2	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
vg0607755407	NA	7.73E-07	mr1655_2	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
vg0607755407	NA	2.52E-07	mr1683_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
vg0607755407	NA	1.45E-06	mr1706_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
vg0607755407	6.66E-06	7.93E-06	mr1833_2	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
vg0607755407	4.73E-06	4.72E-06	mr1833_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
vg0607755407	NA	9.63E-06	mr1840_2	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