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Detailed information for vg0706854122:

Variant ID: vg0706854122 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 6854122
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACACTAGTGTAGGGATAAAAAATTGACAAAAAACCATACAGGTGTAGAGTAGCAAAACTGTCGGTAACATTAGATCTGAAACGGTAAGCAAATGGTTGTT[G/T]
CTGTACTGGTATACTATTTTTAAATTTTAATAGTGGTTGTCATCACCCTAATCTCATGTATAAAACAACCGCTCTTAAAAACTGGTATACCAAAAAACTA

Reverse complement sequence

TAGTTTTTTGGTATACCAGTTTTTAAGAGCGGTTGTTTTATACATGAGATTAGGGTGATGACAACCACTATTAAAATTTAAAAATAGTATACCAGTACAG[C/A]
AACAACCATTTGCTTACCGTTTCAGATCTAATGTTACCGACAGTTTTGCTACTCTACACCTGTATGGTTTTTTGTCAATTTTTTATCCCTACACTAGTGT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	35.30%	8.00%	6.26%	50.44%	NA
All Indica	2759	11.50%	0.20%	7.87%	80.46%	NA
All Japonica	1512	74.30%	23.70%	1.59%	0.40%	NA
Aus	269	37.50%	0.00%	14.13%	48.33%	NA
Indica I	595	6.40%	0.00%	9.75%	83.87%	NA
Indica II	465	14.20%	0.00%	5.81%	80.00%	NA
Indica III	913	11.10%	0.30%	5.26%	83.35%	NA
Indica Intermediate	786	14.20%	0.30%	10.69%	74.81%	NA
Temperate Japonica	767	97.90%	1.20%	0.78%	0.13%	NA
Tropical Japonica	504	30.60%	66.30%	2.78%	0.40%	NA
Japonica Intermediate	241	90.90%	6.20%	1.66%	1.24%	NA
VI/Aromatic	96	84.40%	0.00%	13.54%	2.08%	NA
Intermediate	90	50.00%	16.70%	4.44%	28.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0706854122	G -> DEL	N	N	silent_mutation	Average:81.842; most accessible tissue: Minghui63 root, score: 93.365	N	N	N	N
vg0706854122	G -> T	LOC_Os07g12240.1	upstream_gene_variant ; 2495.0bp to feature; MODIFIER	silent_mutation	Average:81.842; most accessible tissue: Minghui63 root, score: 93.365	N	N	N	N
vg0706854122	G -> T	LOC_Os07g12230.1	downstream_gene_variant ; 732.0bp to feature; MODIFIER	silent_mutation	Average:81.842; most accessible tissue: Minghui63 root, score: 93.365	N	N	N	N
vg0706854122	G -> T	LOC_Os07g12230-LOC_Os07g12240	intergenic_region ; MODIFIER	silent_mutation	Average:81.842; most accessible tissue: Minghui63 root, score: 93.365	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0706854122	NA	1.76E-06	mr1471	Jap_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
vg0706854122	NA	6.83E-09	mr1539	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
vg0706854122	NA	2.67E-06	mr1543	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
vg0706854122	NA	2.82E-07	mr1642	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
vg0706854122	NA	3.23E-06	mr1642	Jap_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
vg0706854122	NA	7.17E-07	mr1671	Jap_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
vg0706854122	NA	9.27E-30	mr1699	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
vg0706854122	NA	1.02E-11	mr1871	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
vg0706854122	3.15E-06	1.90E-09	mr1471_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
vg0706854122	NA	1.23E-09	mr1543_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
vg0706854122	NA	7.17E-06	mr1553_2	Jap_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
vg0706854122	NA	4.99E-09	mr1642_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
vg0706854122	NA	7.86E-15	mr1742_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
vg0706854122	NA	4.61E-09	mr1817_2	Jap_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
vg0706854122	NA	6.02E-08	mr1819_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
vg0706854122	NA	4.94E-10	mr1905_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
vg0706854122	NA	6.29E-08	mr1966_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
vg0706854122	NA	1.50E-07	mr1991_2	Jap_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