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Detailed information for vg0724167005:

Variant ID: vg0724167005 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 24167005
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATGGGACATGTCAGGCTGCACGTCGCCTGACACACGAGCAGCGCACAGGCGCACTAGCCAGTCCCATCGGTCATTTGACCGGTCACAGACCGGTTGAGTG[C/T]
ACTGCACGCCGCATTAAATGTGGCGTGGCGCGACCGCTCGGGACGCCATAAATGCGGGTAAGTGGGCACCTGGAGACGGACATCTAACCCACCGTACGTG

Reverse complement sequence

CACGTACGGTGGGTTAGATGTCCGTCTCCAGGTGCCCACTTACCCGCATTTATGGCGTCCCGAGCGGTCGCGCCACGCCACATTTAATGCGGCGTGCAGT[G/A]
CACTCAACCGGTCTGTGACCGGTCAAATGACCGATGGGACTGGCTAGTGCGCCTGTGCGCTGCTCGTGTGTCAGGCGACGTGCAGCCTGACATGTCCCAT

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	77.70%	22.00%	0.25%	0.00%	NA
All Indica	2759	95.20%	4.60%	0.22%	0.00%	NA
All Japonica	1512	48.50%	51.20%	0.26%	0.00%	NA
Aus	269	93.30%	6.70%	0.00%	0.00%	NA
Indica I	595	95.10%	4.50%	0.34%	0.00%	NA
Indica II	465	91.60%	8.40%	0.00%	0.00%	NA
Indica III	913	97.90%	1.90%	0.22%	0.00%	NA
Indica Intermediate	786	94.10%	5.60%	0.25%	0.00%	NA
Temperate Japonica	767	82.50%	17.20%	0.26%	0.00%	NA
Tropical Japonica	504	8.90%	91.10%	0.00%	0.00%	NA
Japonica Intermediate	241	23.20%	75.90%	0.83%	0.00%	NA
VI/Aromatic	96	10.40%	88.50%	1.04%	0.00%	NA
Intermediate	90	58.90%	40.00%	1.11%	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
vg0724167005	C -> T	LOC_Os07g40300.1	downstream_gene_variant ; 1964.0bp to feature; MODIFIER	silent_mutation	Average:49.388; most accessible tissue: Minghui63 panicle, score: 70.194	N	N	N	N
vg0724167005	C -> T	LOC_Os07g40300-LOC_Os07g40310	intergenic_region ; MODIFIER	silent_mutation	Average:49.388; most accessible tissue: Minghui63 panicle, score: 70.194	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0724167005	3.42E-06	NA	mr1179	Jap_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
vg0724167005	NA	2.12E-08	mr1182	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
vg0724167005	NA	3.76E-07	mr1282	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
vg0724167005	NA	4.04E-07	mr1308	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
vg0724167005	NA	5.19E-07	mr1401	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
vg0724167005	NA	1.35E-06	mr1639	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
vg0724167005	NA	2.93E-06	mr1650	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
vg0724167005	NA	1.47E-06	mr1658	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
vg0724167005	NA	1.85E-06	mr1682	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
vg0724167005	4.06E-06	4.06E-06	mr1853	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
vg0724167005	NA	5.15E-08	mr1182_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
vg0724167005	NA	4.90E-06	mr1282_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
vg0724167005	NA	9.16E-06	mr1416_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
vg0724167005	NA	3.60E-06	mr1959_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