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Detailed information for vg0825960083:

Variant ID: vg0825960083 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 25960083
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CATACATACATACATACATATATATATGCACGCGCGCGACACACACATATATATGTTTATAGGCTGAAACTTAAGGTGTGCACGTACACTTTTTTATGGC[A/G]
CTTAGAATTTTGTCCTGGAGAAAATTCTGTTGACGGTTGTTTTTCCTTGCTGAGATCTACTTGTTGGGGATGATAAAGTTGATTTGTTGCAACCTGAATA

Reverse complement sequence

TATTCAGGTTGCAACAAATCAACTTTATCATCCCCAACAAGTAGATCTCAGCAAGGAAAAACAACCGTCAACAGAATTTTCTCCAGGACAAAATTCTAAG[T/C]
GCCATAAAAAAGTGTACGTGCACACCTTAAGTTTCAGCCTATAAACATATATATGTGTGTGTCGCGCGCGTGCATATATATATGTATGTATGTATGTATG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	79.80%	9.20%	10.98%	0.02%	NA
All Indica	2759	94.90%	0.30%	4.86%	0.04%	NA
All Japonica	1512	59.90%	27.10%	13.10%	0.00%	NA
Aus	269	36.80%	0.70%	62.45%	0.00%	NA
Indica I	595	98.80%	0.30%	0.84%	0.00%	NA
Indica II	465	90.80%	0.00%	9.25%	0.00%	NA
Indica III	913	93.50%	0.30%	6.02%	0.11%	NA
Indica Intermediate	786	95.80%	0.30%	3.94%	0.00%	NA
Temperate Japonica	767	32.90%	49.70%	17.47%	0.00%	NA
Tropical Japonica	504	92.10%	1.20%	6.75%	0.00%	NA
Japonica Intermediate	241	78.40%	9.10%	12.45%	0.00%	NA
VI/Aromatic	96	85.40%	7.30%	7.29%	0.00%	NA
Intermediate	90	74.40%	12.20%	13.33%	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
vg0825960083	A -> G	LOC_Os08g41070.1	missense_variant ; p.Cys1241Arg; MODERATE	nonsynonymous_codon ; C1241R	Average:23.363; most accessible tissue: Minghui63 root, score: 40.262	unknown	unknown	TOLERATED	1.00
vg0825960083	A -> DEL	LOC_Os08g41070.1	N	frameshift_variant	Average:23.363; most accessible tissue: Minghui63 root, score: 40.262	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0825960083	NA	3.33E-08	mr1163	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
vg0825960083	NA	1.44E-07	mr1252	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
vg0825960083	4.91E-06	4.90E-06	mr1261	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
vg0825960083	NA	1.43E-06	mr1310	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
vg0825960083	NA	2.40E-06	mr1880	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
vg0825960083	4.48E-08	NA	mr1926	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
vg0825960083	NA	4.14E-08	mr1926	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
vg0825960083	NA	1.27E-09	mr1977	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
vg0825960083	NA	5.35E-07	mr1977	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
vg0825960083	NA	6.67E-06	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
vg0825960083	7.18E-06	NA	mr1310_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
vg0825960083	NA	2.11E-07	mr1310_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
vg0825960083	9.42E-06	9.41E-06	mr1609_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
vg0825960083	NA	4.02E-07	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