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Detailed information for vg0101824220:

Variant ID: vg0101824220 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 1824220
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GAATTCCTTCGATGGCTAGCTACCACTTCGGCTTGAGGAACGACGACGACGTCTTCTCTGCAACATTACCAGGAAAATGTATTAGTCTAAACGGGCCAAG[C/T]
TACATATATAATCATATATGTATTACCAGTAAATCGTATTAGTATAAACGCGTTCGTTCTCACACTTTTAGTACAAGTGTGTTCACGTTCGTAAGCGTTT

Reverse complement sequence

AAACGCTTACGAACGTGAACACACTTGTACTAAAAGTGTGAGAACGAACGCGTTTATACTAATACGATTTACTGGTAATACATATATGATTATATATGTA[G/A]
CTTGGCCCGTTTAGACTAATACATTTTCCTGGTAATGTTGCAGAGAAGACGTCGTCGTCGTTCCTCAAGCCGAAGTGGTAGCTAGCCATCGAAGGAATTC

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	44.50%	29.90%	18.56%	7.05%	NA
All Indica	2759	60.60%	3.80%	24.72%	10.87%	NA
All Japonica	1512	20.40%	74.10%	3.90%	1.52%	NA
Aus	269	29.40%	23.80%	46.84%	0.00%	NA
Indica I	595	73.80%	0.80%	18.99%	6.39%	NA
Indica II	465	46.50%	2.80%	27.74%	23.01%	NA
Indica III	913	66.60%	5.30%	23.66%	4.49%	NA
Indica Intermediate	786	52.20%	4.80%	28.50%	14.50%	NA
Temperate Japonica	767	6.40%	83.30%	7.43%	2.87%	NA
Tropical Japonica	504	42.30%	57.30%	0.20%	0.20%	NA
Japonica Intermediate	241	19.50%	80.10%	0.41%	0.00%	NA
VI/Aromatic	96	5.20%	93.80%	1.04%	0.00%	NA
Intermediate	90	41.10%	37.80%	10.00%	11.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0101824220	C -> T	LOC_Os01g04140.1	upstream_gene_variant ; 1704.0bp to feature; MODIFIER	silent_mutation	Average:17.197; most accessible tissue: Callus, score: 35.891	N	N	N	N
vg0101824220	C -> T	LOC_Os01g04150.1	downstream_gene_variant ; 1216.0bp to feature; MODIFIER	silent_mutation	Average:17.197; most accessible tissue: Callus, score: 35.891	N	N	N	N
vg0101824220	C -> T	LOC_Os01g04140-LOC_Os01g04150	intergenic_region ; MODIFIER	silent_mutation	Average:17.197; most accessible tissue: Callus, score: 35.891	N	N	N	N
vg0101824220	C -> DEL	N	N	silent_mutation	Average:17.197; most accessible tissue: Callus, score: 35.891	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0101824220	1.53E-06	4.00E-22	Yield	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
vg0101824220	NA	3.98E-08	Yield	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