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Detailed information for vg0621601441:

Variant ID: vg0621601441 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 21601441
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 331. )

Flanking Sequence (100 bp) in Reference Genome:

CACTACCTAAAAAAGTGGCAAAGGCATAACAATTCTTTGCAACAGCATACTACTTGGAAAAAAAGGTCAATATACTTAGTTCGAAAAAGAAACAAGAAAA[G/T]
AAAATCGTGTGGCCTTCTGAACAGTTCAAGACTAGCTAAAATTATATTTATCTTATGACTTACATTTTCGATGACAGGGTTGTCATGCAGGTCTGCACCA

Reverse complement sequence

TGGTGCAGACCTGCATGACAACCCTGTCATCGAAAATGTAAGTCATAAGATAAATATAATTTTAGCTAGTCTTGAACTGTTCAGAAGGCCACACGATTTT[C/A]
TTTTCTTGTTTCTTTTTCGAACTAAGTATATTGACCTTTTTTTCCAAGTAGTATGCTGTTGCAAAGAATTGTTATGCCTTTGCCACTTTTTTAGGTAGTG

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	94.30%	2.40%	2.94%	0.36%	NA
All Indica	2759	97.70%	0.10%	1.88%	0.33%	NA
All Japonica	1512	90.50%	7.50%	1.92%	0.07%	NA
Aus	269	98.10%	0.00%	1.49%	0.37%	NA
Indica I	595	99.20%	0.00%	0.67%	0.17%	NA
Indica II	465	97.60%	0.00%	2.37%	0.00%	NA
Indica III	913	97.00%	0.00%	2.41%	0.55%	NA
Indica Intermediate	786	97.50%	0.30%	1.91%	0.38%	NA
Temperate Japonica	767	94.40%	3.50%	2.09%	0.00%	NA
Tropical Japonica	504	90.70%	9.30%	0.00%	0.00%	NA
Japonica Intermediate	241	78.00%	16.20%	5.39%	0.41%	NA
VI/Aromatic	96	43.80%	0.00%	51.04%	5.21%	NA
Intermediate	90	93.30%	0.00%	5.56%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0621601441	G -> T	LOC_Os06g36700.1	intron_variant ; MODIFIER	silent_mutation	Average:68.144; most accessible tissue: Callus, score: 83.925	N	N	N	N
vg0621601441	G -> DEL	N	N	silent_mutation	Average:68.144; most accessible tissue: Callus, score: 83.925	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0621601441	6.62E-07	6.62E-07	mr1098	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
vg0621601441	NA	9.45E-07	mr1113	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
vg0621601441	NA	3.67E-07	mr1150	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
vg0621601441	NA	2.95E-07	mr1240	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
vg0621601441	1.74E-06	1.74E-06	mr1918	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
vg0621601441	NA	1.09E-07	mr1961	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