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Detailed information for vg0119388504:

Variant ID: vg0119388504 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 19388504
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.02, others allele: 0.00, population size: 113. )

Flanking Sequence (100 bp) in Reference Genome:

ATATATATATATATATATATATATATATATATATATATATATATATATATATATCATATGCGCACAAGCTTCTCTTACACACTCCGTACACACCAAATAA[T/C]
AAATGTCATGAAAAACTATACAAAATATTGAACATTTACTCCTAATAGTATTACACATATATGCAAAGTATCATATTCAAATTCACTATATTTTAGCCAT

Reverse complement sequence

ATGGCTAAAATATAGTGAATTTGAATATGATACTTTGCATATATGTGTAATACTATTAGGAGTAAATGTTCAATATTTTGTATAGTTTTTCATGACATTT[A/G]
TTATTTGGTGTGTACGGAGTGTGTAAGAGAAGCTTGTGCGCATATGATATATATATATATATATATATATATATATATATATATATATATATATATATAT

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	49.10%	10.10%	14.11%	26.62%	NA
All Indica	2759	50.60%	16.40%	22.98%	10.04%	NA
All Japonica	1512	41.30%	1.30%	1.12%	56.28%	NA
Aus	269	73.20%	0.70%	2.97%	23.05%	NA
Indica I	595	48.20%	34.30%	15.63%	1.85%	NA
Indica II	465	79.80%	4.30%	4.95%	10.97%	NA
Indica III	913	32.10%	15.20%	38.23%	14.46%	NA
Indica Intermediate	786	56.50%	11.50%	21.50%	10.56%	NA
Temperate Japonica	767	63.40%	0.40%	1.04%	35.20%	NA
Tropical Japonica	504	15.70%	2.00%	1.39%	80.95%	NA
Japonica Intermediate	241	24.90%	2.50%	0.83%	71.78%	NA
VI/Aromatic	96	55.20%	1.00%	1.04%	42.71%	NA
Intermediate	90	57.80%	4.40%	7.78%	30.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0119388504	T -> DEL	N	N	silent_mutation	Average:29.273; most accessible tissue: Callus, score: 75.052	N	N	N	N
vg0119388504	T -> C	LOC_Os01g35040.1	upstream_gene_variant ; 1327.0bp to feature; MODIFIER	silent_mutation	Average:29.273; most accessible tissue: Callus, score: 75.052	N	N	N	N
vg0119388504	T -> C	LOC_Os01g35030.1	downstream_gene_variant ; 1306.0bp to feature; MODIFIER	silent_mutation	Average:29.273; most accessible tissue: Callus, score: 75.052	N	N	N	N
vg0119388504	T -> C	LOC_Os01g35030-LOC_Os01g35040	intergenic_region ; MODIFIER	silent_mutation	Average:29.273; most accessible tissue: Callus, score: 75.052	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0119388504	NA	8.92E-11	Heading_date	Jap_All	Not	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0119388504	NA	3.57E-09	mr1002	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
vg0119388504	NA	8.96E-07	mr1042	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
vg0119388504	NA	3.92E-07	mr1043	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
vg0119388504	NA	1.76E-07	mr1133	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
vg0119388504	NA	5.13E-09	mr1002_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
vg0119388504	NA	4.22E-08	mr1010_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
vg0119388504	NA	5.51E-06	mr1215_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
vg0119388504	NA	5.65E-07	mr1220_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
vg0119388504	NA	4.82E-06	mr1422_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
vg0119388504	NA	7.18E-07	mr1517_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
vg0119388504	NA	4.19E-07	mr1519_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
vg0119388504	NA	6.13E-06	mr1622_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
vg0119388504	NA	1.12E-06	mr1902_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
vg0119388504	NA	2.96E-06	mr1954_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
vg0119388504	3.51E-06	3.50E-06	mr1972_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