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Detailed information for vg0106608619:

Variant ID: vg0106608619 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 6608619
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.86, C: 0.15, others allele: 0.00, population size: 59. )

Flanking Sequence (100 bp) in Reference Genome:

TTTTGCAAAAAGTTTCTATACGAAAGTTGCTTAAAGAATCAAATTAATCTATTTTGAAATTTTTTTTAGCAAATACTTAATTAATCACACGCTAATGGAC[C/T]
GCTCCATTTTCTGTGTAGGGGAGTTGGGTTCCCAACCGTCTGAAACAAACGGAGACACATGAGCTCATAGACCACCTTGAACACCAGCGGATGGTGGTGA

Reverse complement sequence

TCACCACCATCCGCTGGTGTTCAAGGTGGTCTATGAGCTCATGTGTCTCCGTTTGTTTCAGACGGTTGGGAACCCAACTCCCCTACACAGAAAATGGAGC[G/A]
GTCCATTAGCGTGTGATTAATTAAGTATTTGCTAAAAAAAATTTCAAAATAGATTAATTTGATTCTTTAAGCAACTTTCGTATAGAAACTTTTTGCAAAA

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	61.90%	38.00%	0.11%	0.00%	NA
All Indica	2759	57.20%	42.80%	0.07%	0.00%	NA
All Japonica	1512	83.20%	16.60%	0.20%	0.00%	NA
Aus	269	0.40%	99.60%	0.00%	0.00%	NA
Indica I	595	40.70%	59.20%	0.17%	0.00%	NA
Indica II	465	67.10%	32.70%	0.22%	0.00%	NA
Indica III	913	68.60%	31.40%	0.00%	0.00%	NA
Indica Intermediate	786	50.50%	49.50%	0.00%	0.00%	NA
Temperate Japonica	767	98.00%	2.00%	0.00%	0.00%	NA
Tropical Japonica	504	69.20%	30.40%	0.40%	0.00%	NA
Japonica Intermediate	241	65.10%	34.40%	0.41%	0.00%	NA
VI/Aromatic	96	30.20%	69.80%	0.00%	0.00%	NA
Intermediate	90	68.90%	31.10%	0.00%	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
vg0106608619	C -> T	LOC_Os01g12120.1	upstream_gene_variant ; 1380.0bp to feature; MODIFIER	silent_mutation	Average:51.036; most accessible tissue: Minghui63 panicle, score: 77.956	N	N	N	N
vg0106608619	C -> T	LOC_Os01g12130.1	downstream_gene_variant ; 3724.0bp to feature; MODIFIER	silent_mutation	Average:51.036; most accessible tissue: Minghui63 panicle, score: 77.956	N	N	N	N
vg0106608619	C -> T	LOC_Os01g12120-LOC_Os01g12130	intergenic_region ; MODIFIER	silent_mutation	Average:51.036; most accessible tissue: Minghui63 panicle, score: 77.956	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0106608619	NA	8.86E-07	mr1236	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
vg0106608619	5.38E-06	9.59E-15	mr1769	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
vg0106608619	NA	3.31E-10	mr1951	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
vg0106608619	NA	7.51E-06	mr1159_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
vg0106608619	NA	3.43E-06	mr1236_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
vg0106608619	NA	1.88E-06	mr1236_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
vg0106608619	NA	3.92E-07	mr1723_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
vg0106608619	1.29E-08	NA	mr1769_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
vg0106608619	6.61E-11	8.04E-24	mr1769_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
vg0106608619	NA	1.98E-06	mr1825_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
vg0106608619	NA	7.65E-06	mr1856_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
vg0106608619	2.35E-06	NA	mr1951_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
vg0106608619	1.13E-07	1.83E-09	mr1951_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
vg0106608619	NA	5.50E-06	mr1977_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