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Detailed information for vg0219524344:

Variant ID: vg0219524344 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 19524344
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACATCTCGTGGCTGAACGGGGCTTGTGCTCAGCTTGAAGGCATCGGCGGGCGTATCGACGAGGCCCTGAAGCAGGAATGTCGTTGATCGAGCCGATACGC[C/T]
GGAGGGCACATGTTGGCGTGTATACGAGATCATCGTCCGCAGTTGCACCTCGAGTTCCTTCACGAAGGGTTTTCCCATTCTCGGAGGAATCCTATGGAGA

Reverse complement sequence

TCTCCATAGGATTCCTCCGAGAATGGGAAAACCCTTCGTGAAGGAACTCGAGGTGCAACTGCGGACGATGATCTCGTATACACGCCAACATGTGCCCTCC[G/A]
GCGTATCGGCTCGATCAACGACATTCCTGCTTCAGGGCCTCGTCGATACGCCCGCCGATGCCTTCAAGCTGAGCACAAGCCCCGTTCAGCCACGAGATGT

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	80.60%	1.90%	6.71%	10.79%	NA
All Indica	2759	70.70%	0.20%	10.80%	18.30%	NA
All Japonica	1512	93.80%	5.60%	0.53%	0.07%	NA
Aus	269	98.10%	0.00%	1.86%	0.00%	NA
Indica I	595	73.10%	0.00%	5.71%	21.18%	NA
Indica II	465	83.00%	0.00%	6.24%	10.75%	NA
Indica III	913	56.70%	0.20%	18.18%	24.86%	NA
Indica Intermediate	786	77.90%	0.40%	8.78%	12.98%	NA
Temperate Japonica	767	92.30%	7.70%	0.00%	0.00%	NA
Tropical Japonica	504	98.60%	0.20%	1.19%	0.00%	NA
Japonica Intermediate	241	88.40%	10.40%	0.83%	0.41%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	88.90%	0.00%	6.67%	4.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0219524344	C -> T	LOC_Os02g32870.1	downstream_gene_variant ; 15.0bp to feature; MODIFIER	silent_mutation	Average:39.889; most accessible tissue: Minghui63 flag leaf, score: 75.341	N	N	N	N
vg0219524344	C -> T	LOC_Os02g32880.1	downstream_gene_variant ; 786.0bp to feature; MODIFIER	silent_mutation	Average:39.889; most accessible tissue: Minghui63 flag leaf, score: 75.341	N	N	N	N
vg0219524344	C -> T	LOC_Os02g32870-LOC_Os02g32880	intergenic_region ; MODIFIER	silent_mutation	Average:39.889; most accessible tissue: Minghui63 flag leaf, score: 75.341	N	N	N	N
vg0219524344	C -> DEL	N	N	silent_mutation	Average:39.889; most accessible tissue: Minghui63 flag leaf, score: 75.341	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0219524344	NA	8.87E-10	Grain_weight	Jap_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