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Detailed information for vg0706750438:

Variant ID: vg0706750438 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 6750438
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.92, C: 0.08, others allele: 0.00, population size: 78. )

Flanking Sequence (100 bp) in Reference Genome:

TAATCATAGTTTTACTATGTCAGTTTTACGAGATGAAGATCGAATAGGTGGGCTATAGGTAAAGTCTGTAGATGGCTTTGAGTGAGGTCTGATTAATGTA[T/C]
AAGTGTTTTGAACAATTTTATACATTTGGTAAAACCATGTTACTGCATGTATATACCCATGTTACTGCAAATTACATATTCTATTACTGTATATGGAGTG

Reverse complement sequence

CACTCCATATACAGTAATAGAATATGTAATTTGCAGTAACATGGGTATATACATGCAGTAACATGGTTTTACCAAATGTATAAAATTGTTCAAAACACTT[A/G]
TACATTAATCAGACCTCACTCAAAGCCATCTACAGACTTTACCTATAGCCCACCTATTCGATCTTCATCTCGTAAAACTGACATAGTAAAACTATGATTA

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	37.90%	1.10%	11.89%	49.03%	NA
All Indica	2759	4.20%	1.70%	15.04%	78.98%	NA
All Japonica	1512	99.40%	0.00%	0.13%	0.46%	NA
Aus	269	11.50%	2.20%	51.30%	34.94%	NA
Indica I	595	1.50%	1.80%	3.36%	93.28%	NA
Indica II	465	6.90%	2.40%	6.88%	83.87%	NA
Indica III	913	3.20%	1.00%	28.04%	67.80%	NA
Indica Intermediate	786	6.00%	2.20%	13.61%	78.24%	NA
Temperate Japonica	767	99.60%	0.00%	0.00%	0.39%	NA
Tropical Japonica	504	99.60%	0.00%	0.20%	0.20%	NA
Japonica Intermediate	241	98.30%	0.00%	0.41%	1.24%	NA
VI/Aromatic	96	93.80%	0.00%	1.04%	5.21%	NA
Intermediate	90	57.80%	0.00%	6.67%	35.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0706750438	T -> DEL	N	N	silent_mutation	Average:16.377; most accessible tissue: Callus, score: 22.231	N	N	N	N
vg0706750438	T -> C	LOC_Os07g12080.1	upstream_gene_variant ; 4094.0bp to feature; MODIFIER	silent_mutation	Average:16.377; most accessible tissue: Callus, score: 22.231	N	N	N	N
vg0706750438	T -> C	LOC_Os07g12090.1	upstream_gene_variant ; 3275.0bp to feature; MODIFIER	silent_mutation	Average:16.377; most accessible tissue: Callus, score: 22.231	N	N	N	N
vg0706750438	T -> C	LOC_Os07g12100.1	intron_variant ; MODIFIER	silent_mutation	Average:16.377; most accessible tissue: Callus, score: 22.231	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0706750438	NA	4.11E-06	mr1103	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
vg0706750438	NA	9.46E-30	mr1107	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
vg0706750438	NA	9.71E-08	mr1107	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
vg0706750438	8.40E-06	NA	mr1076_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
vg0706750438	NA	3.46E-35	mr1082_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
vg0706750438	2.64E-06	NA	mr1082_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
vg0706750438	3.33E-06	NA	mr1083_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
vg0706750438	NA	7.86E-32	mr1085_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
vg0706750438	NA	3.38E-66	mr1103_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
vg0706750438	3.60E-06	NA	mr1103_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
vg0706750438	NA	1.58E-35	mr1107_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
vg0706750438	NA	4.23E-42	mr1145_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
vg0706750438	NA	1.26E-11	mr1216_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
vg0706750438	NA	2.54E-24	mr1233_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
vg0706750438	NA	1.56E-38	mr1264_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
vg0706750438	NA	4.71E-07	mr1408_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
vg0706750438	NA	8.85E-44	mr1437_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
vg0706750438	NA	7.49E-23	mr1609_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
vg0706750438	NA	8.48E-32	mr1841_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
vg0706750438	NA	1.29E-06	mr1915_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
vg0706750438	NA	6.84E-09	mr1947_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