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Detailed information for vg0313207043:

Variant ID: vg0313207043 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 13207043
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TAGCCCCCAGCCGTGAAGTTGGAAAGTTTATTTCCGATTACACGGCTTGGTTAATACGCATGGCGAGAACTCTTACACGACCAGATCTTACATGGTCTTT[T/C]
GTCTCTACAGGATCCGACAAGGTCTTATCGGCTCTGGGCGGCCCCAGCTGAAGTTCCCTTAGGTTCCTCGGAGGCCTTGTTAAGACAGCGTAAAGGGACA

Reverse complement sequence

TGTCCCTTTACGCTGTCTTAACAAGGCCTCCGAGGAACCTAAGGGAACTTCAGCTGGGGCCGCCCAGAGCCGATAAGACCTTGTCGGATCCTGTAGAGAC[A/G]
AAAGACCATGTAAGATCTGGTCGTGTAAGAGTTCTCGCCATGCGTATTAACCAAGCCGTGTAATCGGAAATAAACTTTCCAACTTCACGGCTGGGGGCTA

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	39.90%	18.50%	31.95%	9.61%	NA
All Indica	2759	32.60%	0.30%	51.79%	15.37%	NA
All Japonica	1512	43.20%	56.30%	0.26%	0.20%	NA
Aus	269	75.50%	1.10%	16.73%	6.69%	NA
Indica I	595	22.40%	0.30%	56.30%	21.01%	NA
Indica II	465	61.50%	0.20%	33.33%	4.95%	NA
Indica III	913	26.00%	0.00%	57.83%	16.21%	NA
Indica Intermediate	786	30.90%	0.50%	52.29%	16.28%	NA
Temperate Japonica	767	4.30%	95.60%	0.00%	0.13%	NA
Tropical Japonica	504	91.50%	7.70%	0.60%	0.20%	NA
Japonica Intermediate	241	66.00%	33.20%	0.41%	0.41%	NA
VI/Aromatic	96	86.50%	1.00%	10.42%	2.08%	NA
Intermediate	90	54.40%	13.30%	24.44%	7.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0313207043	T -> C	LOC_Os03g22840.1	downstream_gene_variant ; 457.0bp to feature; MODIFIER	silent_mutation	Average:23.981; most accessible tissue: Minghui63 flag leaf, score: 32.882	N	N	N	N
vg0313207043	T -> C	LOC_Os03g22850.1	downstream_gene_variant ; 709.0bp to feature; MODIFIER	silent_mutation	Average:23.981; most accessible tissue: Minghui63 flag leaf, score: 32.882	N	N	N	N
vg0313207043	T -> C	LOC_Os03g22840-LOC_Os03g22850	intergenic_region ; MODIFIER	silent_mutation	Average:23.981; most accessible tissue: Minghui63 flag leaf, score: 32.882	N	N	N	N
vg0313207043	T -> DEL	N	N	silent_mutation	Average:23.981; most accessible tissue: Minghui63 flag leaf, score: 32.882	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0313207043	NA	4.17E-11	Spikelet_length	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
vg0313207043	NA	4.30E-06	mr1330	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
vg0313207043	NA	9.49E-07	mr1584	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
vg0313207043	NA	2.43E-13	mr1879	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
vg0313207043	1.29E-06	NA	mr1071_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
vg0313207043	2.16E-07	NA	mr1080_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
vg0313207043	NA	1.57E-09	mr1087_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
vg0313207043	1.07E-06	NA	mr1100_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
vg0313207043	1.13E-06	NA	mr1203_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
vg0313207043	NA	2.69E-06	mr1250_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
vg0313207043	NA	8.75E-08	mr1308_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
vg0313207043	NA	2.16E-09	mr1350_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
vg0313207043	NA	1.22E-20	mr1361_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
vg0313207043	NA	9.93E-13	mr1361_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
vg0313207043	NA	1.40E-12	mr1368_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
vg0313207043	NA	8.45E-06	mr1404_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
vg0313207043	NA	7.53E-10	mr1584_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
vg0313207043	9.22E-07	NA	mr1619_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
vg0313207043	NA	4.52E-06	mr1730_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
vg0313207043	NA	6.77E-11	mr1789_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
vg0313207043	NA	1.33E-07	mr1794_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
vg0313207043	6.29E-06	NA	mr1795_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
vg0313207043	NA	2.55E-06	mr1853_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
vg0313207043	NA	2.09E-08	mr1952_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