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Detailed information for vg0203899414:

Variant ID: vg0203899414 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 3899414
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CTGCTCTTCCCGGGTACTCTTGTCTTCCTCCAGTGTACCAAGATACTTGGAACTCTCTTCCAATCGGAGATGAAGCAGTACAAGCCTTGGAGTTGTTGGA[C/T]
CGTATGTTAAATCTTAAAGAACAAGGTTTACAGGGAGAGCAGATCACTCGGCACTTCATCAAATGCCGACTGGCGCCAATCAAGGAAAGATCCCGCACAG

Reverse complement sequence

CTGTGCGGGATCTTTCCTTGATTGGCGCCAGTCGGCATTTGATGAAGTGCCGAGTGATCTGCTCTCCCTGTAAACCTTGTTCTTTAAGATTTAACATACG[G/A]
TCCAACAACTCCAAGGCTTGTACTGCTTCATCTCCGATTGGAAGAGAGTTCCAAGTATCTTGGTACACTGGAGGAAGACAAGAGTACCCGGGAAGAGCAG

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	13.60%	1.10%	22.28%	63.10%	NA
All Indica	2759	2.40%	1.70%	22.36%	73.58%	NA
All Japonica	1512	36.70%	0.00%	20.50%	42.79%	NA
Aus	269	0.70%	0.00%	9.29%	89.96%	NA
Indica I	595	1.70%	2.70%	20.34%	75.29%	NA
Indica II	465	5.80%	1.90%	16.13%	76.13%	NA
Indica III	913	0.70%	0.70%	26.51%	72.18%	NA
Indica Intermediate	786	2.80%	2.00%	22.77%	72.39%	NA
Temperate Japonica	767	63.10%	0.00%	6.91%	29.99%	NA
Tropical Japonica	504	3.20%	0.00%	31.35%	65.48%	NA
Japonica Intermediate	241	22.80%	0.00%	41.08%	36.10%	NA
VI/Aromatic	96	0.00%	2.10%	83.33%	14.58%	NA
Intermediate	90	21.10%	1.10%	23.33%	54.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0203899414	C -> T	LOC_Os02g07530.1	synonymous_variant ; p.Asp206Asp; LOW	synonymous_codon	Average:6.368; most accessible tissue: Minghui63 flower, score: 11.139	N	N	N	N
vg0203899414	C -> DEL	LOC_Os02g07530.1	N	frameshift_variant	Average:6.368; most accessible tissue: Minghui63 flower, score: 11.139	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0203899414	6.44E-08	NA	Grain_weight	All	YES	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
vg0203899414	NA	2.13E-11	Plant_height	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
vg0203899414	NA	9.40E-17	Spikelet_length	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
vg0203899414	NA	2.43E-12	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
vg0203899414	NA	2.30E-21	mr1163	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
vg0203899414	NA	1.72E-07	mr1163	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
vg0203899414	NA	1.25E-06	mr1252	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
vg0203899414	NA	1.15E-06	mr1704	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
vg0203899414	NA	1.15E-06	mr1815	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
vg0203899414	NA	1.76E-06	mr1129_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
vg0203899414	NA	4.38E-08	mr1446_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
vg0203899414	NA	7.55E-06	mr1446_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
vg0203899414	NA	1.39E-08	mr1471_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
vg0203899414	NA	4.29E-11	mr1486_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
vg0203899414	NA	1.67E-06	mr1588_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
vg0203899414	NA	2.99E-12	mr1722_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
vg0203899414	NA	1.00E-06	mr1722_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