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Detailed information for vg0419748195:

Variant ID: vg0419748195 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 19748195
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AATTGATCATGATGACGGAGGATAGTGTATTGTTGAGCATTCCTCAAATTAAGCACAAATTAGATGGTGGAATCGAGAAGACTCCCATCATCACTTGCCT[C/T]
ATCATCTTCACCATTGCCACTCCCATTGTCATCACCATCATCACTTACTTCTATCTCATCACCCTCAACATTTTCCATATTGTCATCATCACTTTGAACA

Reverse complement sequence

TGTTCAAAGTGATGATGACAATATGGAAAATGTTGAGGGTGATGAGATAGAAGTAAGTGATGATGGTGATGACAATGGGAGTGGCAATGGTGAAGATGAT[G/A]
AGGCAAGTGATGATGGGAGTCTTCTCGATTCCACCATCTAATTTGTGCTTAATTTGAGGAATGCTCAACAATACACTATCCTCCGTCATCATGATCAATT

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	70.10%	1.70%	4.89%	23.25%	NA
All Indica	2759	54.90%	0.00%	6.27%	38.82%	NA
All Japonica	1512	92.70%	5.20%	1.85%	0.20%	NA
Aus	269	84.00%	0.00%	9.29%	6.69%	NA
Indica I	595	36.30%	0.00%	7.39%	56.30%	NA
Indica II	465	45.20%	0.00%	6.67%	48.17%	NA
Indica III	913	73.20%	0.00%	5.70%	21.14%	NA
Indica Intermediate	786	53.60%	0.00%	5.85%	40.59%	NA
Temperate Japonica	767	87.10%	9.60%	3.13%	0.13%	NA
Tropical Japonica	504	99.00%	0.00%	0.60%	0.40%	NA
Japonica Intermediate	241	97.50%	2.10%	0.41%	0.00%	NA
VI/Aromatic	96	97.90%	0.00%	0.00%	2.08%	NA
Intermediate	90	86.70%	2.20%	5.56%	5.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0419748195	C -> DEL	N	N	silent_mutation	Average:8.087; most accessible tissue: Callus, score: 28.871	N	N	N	N
vg0419748195	C -> T	LOC_Os04g32750.1	intron_variant ; MODIFIER	silent_mutation	Average:8.087; most accessible tissue: Callus, score: 28.871	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0419748195	7.08E-10	6.38E-16	Awn_length	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