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Detailed information for vg0601074897:

Variant ID: vg0601074897 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 1074897
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGTTAGAAGACCAAGGCTCAGACCCCAGTTGAGTTTTGCCTGTGGAGTGGAGCTGAAGCCCCGTTAGGATCACCTTTTTCCGCTGCTGTCGTTTCTTTTC[G/A]
GTGCGAGGACTAAGAGCCTCTTCTGTAAGTATTTTACGCTTTATTTACGTTTGGAACTGTATATTACTTGTCGTTTTGTGTACCCTGGCTGGTCCTGGAT

Reverse complement sequence

ATCCAGGACCAGCCAGGGTACACAAAACGACAAGTAATATACAGTTCCAAACGTAAATAAAGCGTAAAATACTTACAGAAGAGGCTCTTAGTCCTCGCAC[C/T]
GAAAAGAAACGACAGCAGCGGAAAAAGGTGATCCTAACGGGGCTTCAGCTCCACTCCACAGGCAAAACTCAACTGGGGTCTGAGCCTTGGTCTTCTAACT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	57.10%	11.20%	1.54%	30.11%	NA
All Indica	2759	42.40%	11.80%	2.32%	43.46%	NA
All Japonica	1512	94.20%	0.40%	0.20%	5.22%	NA
Aus	269	9.70%	40.90%	1.49%	47.96%	NA
Indica I	595	70.10%	5.50%	1.01%	23.36%	NA
Indica II	465	61.90%	5.40%	2.80%	29.89%	NA
Indica III	913	13.90%	19.30%	2.19%	64.62%	NA
Indica Intermediate	786	43.10%	11.60%	3.18%	42.11%	NA
Temperate Japonica	767	99.70%	0.10%	0.00%	0.13%	NA
Tropical Japonica	504	84.70%	0.20%	0.60%	14.48%	NA
Japonica Intermediate	241	96.30%	1.70%	0.00%	2.07%	NA
VI/Aromatic	96	16.70%	82.30%	0.00%	1.04%	NA
Intermediate	90	70.00%	11.10%	2.22%	16.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0601074897	G -> A	LOC_Os06g02910.1	downstream_gene_variant ; 3305.0bp to feature; MODIFIER	silent_mutation	Average:41.424; most accessible tissue: Zhenshan97 panicle, score: 68.538	N	N	N	N
vg0601074897	G -> A	LOC_Os06g02930.1	downstream_gene_variant ; 3150.0bp to feature; MODIFIER	silent_mutation	Average:41.424; most accessible tissue: Zhenshan97 panicle, score: 68.538	N	N	N	N
vg0601074897	G -> A	LOC_Os06g02920.1	intron_variant ; MODIFIER	silent_mutation	Average:41.424; most accessible tissue: Zhenshan97 panicle, score: 68.538	N	N	N	N
vg0601074897	G -> DEL	N	N	silent_mutation	Average:41.424; most accessible tissue: Zhenshan97 panicle, score: 68.538	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0601074897	1.38E-06	NA	Heading_date	Ind_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