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Detailed information for vg0405360103:

Variant ID: vg0405360103 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 5360103
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 81. )

Flanking Sequence (100 bp) in Reference Genome:

TAGAATATCGCAAACCACCATGGCATTCATCACATAAAATCTAAATCAACTCCATGTTTCTACTAATCTATGTATTATTATATAATAAAAGTCCATTAAA[C/T]
TTCCTATAAACGCTCCTAAGCCGCCACATGGCACTCCTACAAAAGCTATAAAGCCGTTATGTGGCACTCAAATAAATTATAGAAATTATGTAAATTATGT

Reverse complement sequence

ACATAATTTACATAATTTCTATAATTTATTTGAGTGCCACATAACGGCTTTATAGCTTTTGTAGGAGTGCCATGTGGCGGCTTAGGAGCGTTTATAGGAA[G/A]
TTTAATGGACTTTTATTATATAATAATACATAGATTAGTAGAAACATGGAGTTGATTTAGATTTTATGTGATGAATGCCATGGTGGTTTGCGATATTCTA

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	59.60%	40.00%	0.30%	0.06%	NA
All Indica	2759	81.80%	17.70%	0.43%	0.07%	NA
All Japonica	1512	10.40%	89.60%	0.07%	0.00%	NA
Aus	269	98.50%	0.70%	0.37%	0.37%	NA
Indica I	595	93.10%	5.50%	1.34%	0.00%	NA
Indica II	465	87.50%	12.30%	0.22%	0.00%	NA
Indica III	913	69.40%	30.20%	0.11%	0.22%	NA
Indica Intermediate	786	84.40%	15.40%	0.25%	0.00%	NA
Temperate Japonica	767	8.20%	91.80%	0.00%	0.00%	NA
Tropical Japonica	504	13.90%	86.10%	0.00%	0.00%	NA
Japonica Intermediate	241	10.00%	89.60%	0.41%	0.00%	NA
VI/Aromatic	96	88.50%	11.50%	0.00%	0.00%	NA
Intermediate	90	58.90%	41.10%	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
vg0405360103	C -> DEL	N	N	silent_mutation	Average:39.813; most accessible tissue: Minghui63 flag leaf, score: 53.617	N	N	N	N
vg0405360103	C -> T	LOC_Os04g09950.1	downstream_gene_variant ; 2312.0bp to feature; MODIFIER	silent_mutation	Average:39.813; most accessible tissue: Minghui63 flag leaf, score: 53.617	N	N	N	N
vg0405360103	C -> T	LOC_Os04g09960.1	downstream_gene_variant ; 364.0bp to feature; MODIFIER	silent_mutation	Average:39.813; most accessible tissue: Minghui63 flag leaf, score: 53.617	N	N	N	N
vg0405360103	C -> T	LOC_Os04g09960-LOC_Os04g09980	intergenic_region ; MODIFIER	silent_mutation	Average:39.813; most accessible tissue: Minghui63 flag leaf, score: 53.617	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0405360103	NA	7.24E-11	Grain_weight	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
vg0405360103	NA	3.21E-10	mr1023	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
vg0405360103	9.95E-07	1.19E-20	mr1035	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
vg0405360103	NA	3.99E-06	mr1035	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
vg0405360103	NA	2.06E-47	mr1136	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
vg0405360103	NA	3.81E-06	mr1203	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
vg0405360103	NA	7.36E-07	mr1395	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
vg0405360103	4.40E-06	NA	mr1419	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
vg0405360103	NA	8.59E-07	mr1489	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
vg0405360103	NA	9.33E-06	mr1618	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
vg0405360103	3.39E-06	3.26E-17	mr1626	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
vg0405360103	NA	8.94E-06	mr1626	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
vg0405360103	1.72E-06	1.10E-32	mr1631	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
vg0405360103	7.96E-06	1.30E-06	mr1631	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
vg0405360103	NA	2.59E-09	mr1637	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
vg0405360103	NA	3.49E-13	mr1740	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
vg0405360103	NA	7.29E-10	mr1905	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
vg0405360103	NA	1.46E-16	mr1035_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
vg0405360103	NA	9.80E-18	mr1062_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
vg0405360103	NA	1.96E-52	mr1136_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
vg0405360103	NA	1.36E-18	mr1167_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
vg0405360103	NA	1.18E-29	mr1631_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