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Detailed information for vg0720474327:

Variant ID: vg0720474327 (JBrowse)	Variation Type: INDEL
Chromosome: chr07	Position: 20474327
Reference Allele: AGCGTGCGCGTAGTGGGTGGTG	Alternative Allele: A,CGCGTGCGCGTAGTGGGTGGTG
Primary Allele: AGCGTGCGCGTAGTGGGTGG TG	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GGGTGGCTAGTGGCTCGTGGGTGCACAGAAGGGGACACGAAGGGATCAGCGTGCGCGTAGTGGGTGGTGGATGATGTTGCGTAGACGACGAGTCAAGATG[AGCGTGCGCGTAGTGGGTGGTG/A,CGCGTGCGCGTAGTGGGTGGTG]
GATGATGTTGCGTAGACGACGAGTCAAGATAAGCGTGGGGTGTTAGGTGATCATTAATCTATCCCGTTAGGACGGTATTCCGTTTTATAGATTTTCTGTT

Reverse complement sequence

AACAGAAAATCTATAAAACGGAATACCGTCCTAACGGGATAGATTAATGATCACCTAACACCCCACGCTTATCTTGACTCGTCGTCTACGCAACATCATC[CACCACCCACTACGCGCACGCT/T,CACCACCCACTACGCGCACGCG]
CATCTTGACTCGTCGTCTACGCAACATCATCCACCACCCACTACGCGCACGCTGATCCCTTCGTGTCCCCTTCTGTGCACCCACGAGCCACTAGCCACCC

Allele Frequencies:

Populations	Population Size	Frequency of AGCGTGCGCGTAGTGGGTGG TG(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	81.60%	0.40%	2.81%	14.92%	CGCGTGCGCGTAGTGGGTGGTG: 0.28%
All Indica	2759	81.40%	0.70%	4.13%	13.81%	NA
All Japonica	1512	98.40%	0.00%	0.00%	0.73%	CGCGTGCGCGTAGTGGGTGGTG: 0.86%
Aus	269	11.90%	0.00%	4.83%	83.27%	NA
Indica I	595	90.60%	1.50%	4.03%	3.87%	NA
Indica II	465	79.40%	0.60%	4.30%	15.70%	NA
Indica III	913	75.70%	0.00%	4.27%	20.04%	NA
Indica Intermediate	786	82.30%	0.80%	3.94%	12.98%	NA
Temperate Japonica	767	99.60%	0.00%	0.00%	0.39%	NA
Tropical Japonica	504	97.60%	0.00%	0.00%	0.00%	CGCGTGCGCGTAGTGGGTGGTG: 2.38%
Japonica Intermediate	241	96.30%	0.00%	0.00%	3.32%	CGCGTGCGCGTAGTGGGTGGTG: 0.41%
VI/Aromatic	96	20.80%	0.00%	1.04%	78.12%	NA
Intermediate	90	78.90%	0.00%	5.56%	15.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0720474327	AGCGTGCGCGTAGTGGGTGGTG -> DEL	N	N	silent_mutation	Average:54.113; most accessible tissue: Zhenshan97 young leaf, score: 65.28	N	N	N	N
vg0720474327	AGCGTGCGCGTAGTGGGTGGTG -> CGCGTGCGCGTAGTGGGTGGTG	LOC_Os07g34220.1	downstream_gene_variant ; 2747.0bp to feature; MODIFIER	silent_mutation	Average:54.113; most accessible tissue: Zhenshan97 young leaf, score: 65.28	N	N	N	N
vg0720474327	AGCGTGCGCGTAGTGGGTGGTG -> CGCGTGCGCGTAGTGGGTGGTG	LOC_Os07g34210-LOC_Os07g34220	intergenic_region ; MODIFIER	silent_mutation	Average:54.113; most accessible tissue: Zhenshan97 young leaf, score: 65.28	N	N	N	N
vg0720474327	AGCGTGCGCGTAGTGGGTGGTG -> A	LOC_Os07g34220.1	downstream_gene_variant ; 2746.0bp to feature; MODIFIER	silent_mutation	Average:54.113; most accessible tissue: Zhenshan97 young leaf, score: 65.28	N	N	N	N
vg0720474327	AGCGTGCGCGTAGTGGGTGGTG -> A	LOC_Os07g34210-LOC_Os07g34220	intergenic_region ; MODIFIER	silent_mutation	Average:54.113; most accessible tissue: Zhenshan97 young leaf, score: 65.28	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0720474327	2.45E-06	2.45E-06	mr1846_2	Jap_All	YES	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251