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Detailed information for vg1004077056:

Variant ID: vg1004077056 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 4077056
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, others allele: 0.00, population size: 103. )

Flanking Sequence (100 bp) in Reference Genome:

TTCGTCCACCAATATAAGGGATTCTAGAGTACTACTTATCCCATCAATCACATTGATTTCATTAAAAAAATTCGTATTATCCCCGACTACACTCACACAT[T/C]
CAGCATCTCATTTAACCAAGGGCATCATTGTTTTTCTCTGCATACCCAAAGTCTGTAGTATTTGTTGATGGAGGGAATACACAAAAGACCACCCATTTGT

Reverse complement sequence

ACAAATGGGTGGTCTTTTGTGTATTCCCTCCATCAACAAATACTACAGACTTTGGGTATGCAGAGAAAAACAATGATGCCCTTGGTTAAATGAGATGCTG[A/G]
ATGTGTGAGTGTAGTCGGGGATAATACGAATTTTTTTAATGAAATCAATGTGATTGATGGGATAAGTAGTACTCTAGAATCCCTTATATTGGTGGACGAA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	63.30%	36.50%	0.19%	0.00%	NA
All Indica	2759	43.30%	56.40%	0.29%	0.00%	NA
All Japonica	1512	90.80%	9.20%	0.00%	0.00%	NA
Aus	269	97.00%	3.00%	0.00%	0.00%	NA
Indica I	595	43.40%	56.00%	0.67%	0.00%	NA
Indica II	465	50.80%	49.20%	0.00%	0.00%	NA
Indica III	913	44.60%	55.30%	0.11%	0.00%	NA
Indica Intermediate	786	37.30%	62.30%	0.38%	0.00%	NA
Temperate Japonica	767	83.60%	16.40%	0.00%	0.00%	NA
Tropical Japonica	504	99.60%	0.40%	0.00%	0.00%	NA
Japonica Intermediate	241	95.40%	4.60%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	75.60%	23.30%	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
vg1004077056	T -> C	LOC_Os10g07554.1	downstream_gene_variant ; 3114.0bp to feature; MODIFIER	silent_mutation	Average:40.339; most accessible tissue: Callus, score: 70.731	N	N	N	N
vg1004077056	T -> C	LOC_Os10g07556.1	intron_variant ; MODIFIER	silent_mutation	Average:40.339; most accessible tissue: Callus, score: 70.731	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1004077056	NA	9.80E-08	mr1585	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
vg1004077056	NA	6.50E-06	mr1971	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
vg1004077056	6.24E-06	1.52E-09	mr1305_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
vg1004077056	NA	2.20E-07	mr1321_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
vg1004077056	NA	5.59E-06	mr1380_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
vg1004077056	NA	1.47E-06	mr1380_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
vg1004077056	NA	8.58E-06	mr1409_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
vg1004077056	NA	2.81E-07	mr1559_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
vg1004077056	NA	7.63E-07	mr1561_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
vg1004077056	NA	1.18E-06	mr1561_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
vg1004077056	NA	7.93E-11	mr1585_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
vg1004077056	NA	3.37E-06	mr1703_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
vg1004077056	NA	2.98E-06	mr1723_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
vg1004077056	NA	2.59E-08	mr1765_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
vg1004077056	NA	1.93E-09	mr1875_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
vg1004077056	NA	2.18E-07	mr1875_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
vg1004077056	NA	1.47E-06	mr1908_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
vg1004077056	NA	4.33E-06	mr1908_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
vg1004077056	NA	3.34E-06	mr1994_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
vg1004077056	NA	8.05E-08	mr1994_2	Ind_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