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Detailed information for vg0100975309:

Variant ID: vg0100975309 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 975309
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GACTTTTGGGTCCTCACTCGCTCTGGGAAATGGAAACCTTGCCTTGACCGGGTTAAACGAACCGCCTCCGGCTGTGAAGAGAGGCTAAACAGCCTCTCAT[C/A]
ATCATGATGTGACAGGGGATGTCAGGCGGCACACCGCCTGACATGCAACCAGTGTGCAGGCGCACTACCCTGGTCACGTCAGTCATTCGACCGGTCGCAG

Reverse complement sequence

CTGCGACCGGTCGAATGACTGACGTGACCAGGGTAGTGCGCCTGCACACTGGTTGCATGTCAGGCGGTGTGCCGCCTGACATCCCCTGTCACATCATGAT[G/T]
ATGAGAGGCTGTTTAGCCTCTCTTCACAGCCGGAGGCGGTTCGTTTAACCCGGTCAAGGCAAGGTTTCCATTTCCCAGAGCGAGTGAGGACCCAAAAGTC

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	35.00%	7.90%	2.20%	54.91%	NA
All Indica	2759	24.20%	0.80%	1.85%	73.07%	NA
All Japonica	1512	50.70%	18.40%	0.53%	30.36%	NA
Aus	269	56.90%	0.00%	16.36%	26.77%	NA
Indica I	595	12.90%	0.20%	1.51%	85.38%	NA
Indica II	465	7.10%	2.40%	2.58%	87.96%	NA
Indica III	913	36.10%	0.20%	1.75%	61.88%	NA
Indica Intermediate	786	29.10%	1.10%	1.78%	67.94%	NA
Temperate Japonica	767	70.50%	23.10%	0.26%	6.13%	NA
Tropical Japonica	504	14.30%	8.70%	1.19%	75.79%	NA
Japonica Intermediate	241	63.90%	23.70%	0.00%	12.45%	NA
VI/Aromatic	96	29.20%	63.50%	1.04%	6.25%	NA
Intermediate	90	40.00%	13.30%	0.00%	46.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0100975309	C -> A	LOC_Os01g02780.1	upstream_gene_variant ; 1982.0bp to feature; MODIFIER	silent_mutation	Average:31.614; most accessible tissue: Minghui63 young leaf, score: 65.161	N	N	N	N
vg0100975309	C -> A	LOC_Os01g02790.1	upstream_gene_variant ; 1457.0bp to feature; MODIFIER	silent_mutation	Average:31.614; most accessible tissue: Minghui63 young leaf, score: 65.161	N	N	N	N
vg0100975309	C -> A	LOC_Os01g02780-LOC_Os01g02790	intergenic_region ; MODIFIER	silent_mutation	Average:31.614; most accessible tissue: Minghui63 young leaf, score: 65.161	N	N	N	N
vg0100975309	C -> DEL	N	N	silent_mutation	Average:31.614; most accessible tissue: Minghui63 young leaf, score: 65.161	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0100975309	1.66E-07	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