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Detailed information for vg0605415219:

Variant ID: vg0605415219 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 5415219
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.54, T: 0.45, others allele: 0.00, population size: 99. )

Flanking Sequence (100 bp) in Reference Genome:

AACACTTTTTAATTTTTAAGTAGTAGAGATTGAGATAGAGATACAGATAGAGATAGAGATAGAGAAACGGAAAACTTTTTTTGAAACTTTTTTTTTGGAA[C/T]
CGGACAGAAAAAATTTTACGTTTGTTTTTTACCGCATAGATGGAATCGGATTCAATTTGTTTTTTTACCACGCCGTGTCACATATAATAGGATTCGATTT

Reverse complement sequence

AAATCGAATCCTATTATATGTGACACGGCGTGGTAAAAAAACAAATTGAATCCGATTCCATCTATGCGGTAAAAAACAAACGTAAAATTTTTTCTGTCCG[G/A]
TTCCAAAAAAAAAGTTTCAAAAAAAGTTTTCCGTTTCTCTATCTCTATCTCTATCTGTATCTCTATCTCAATCTCTACTACTTAAAAATTAAAAAGTGTT

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	72.30%	24.60%	1.74%	1.31%	NA
All Indica	2759	78.50%	16.80%	2.50%	2.25%	NA
All Japonica	1512	64.00%	35.40%	0.60%	0.00%	NA
Aus	269	81.80%	18.20%	0.00%	0.00%	NA
Indica I	595	52.30%	32.90%	7.73%	7.06%	NA
Indica II	465	96.30%	1.70%	1.08%	0.86%	NA
Indica III	913	84.10%	15.90%	0.00%	0.00%	NA
Indica Intermediate	786	81.20%	14.50%	2.29%	2.04%	NA
Temperate Japonica	767	97.00%	2.90%	0.13%	0.00%	NA
Tropical Japonica	504	18.50%	80.40%	1.19%	0.00%	NA
Japonica Intermediate	241	53.90%	45.20%	0.83%	0.00%	NA
VI/Aromatic	96	13.50%	85.40%	1.04%	0.00%	NA
Intermediate	90	58.90%	37.80%	3.33%	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
vg0605415219	C -> T	LOC_Os06g10510-LOC_Os06g10520	intergenic_region ; MODIFIER	silent_mutation	Average:32.172; most accessible tissue: Minghui63 panicle, score: 68.46	N	N	N	N
vg0605415219	C -> DEL	N	N	silent_mutation	Average:32.172; most accessible tissue: Minghui63 panicle, score: 68.46	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0605415219	4.30E-10	1.22E-23	mr1201	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
vg0605415219	1.67E-17	7.66E-49	mr1201	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
vg0605415219	2.95E-08	3.20E-18	mr1219	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
vg0605415219	6.08E-16	4.65E-41	mr1219	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
vg0605415219	5.91E-09	1.19E-18	mr1274	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
vg0605415219	1.66E-17	1.30E-41	mr1274	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
vg0605415219	NA	6.82E-06	mr1544	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
vg0605415219	6.97E-12	6.77E-23	mr1201_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
vg0605415219	3.40E-19	3.10E-42	mr1201_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
vg0605415219	8.34E-08	1.09E-16	mr1219_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
vg0605415219	1.33E-15	3.81E-35	mr1219_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
vg0605415219	6.68E-08	1.39E-16	mr1274_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
vg0605415219	2.12E-17	1.82E-40	mr1274_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