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Detailed information for vg0623461786:

Variant ID: vg0623461786 (JBrowse)	Variation Type: INDEL
Chromosome: chr06	Position: 23461786
Reference Allele: G	Alternative Allele: A,GGATAAAAAAAACCAATTACATAGAAATTTCATCATATCAAATA,GGACAAAAAAAACCAATTACATAGAAATTTCATCATATCAAATA
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AATCCCTTTTGATTATTCCGTACATAACGCATGGAAAAGAATTGGAGTAGGGGCAGTCTTTAGTTCACTTCAAACTTTAAAAAAATTCATCATATTAAAT[G/A,GGATAAAAAAAACCAATTACATAGAAATTTCATCATATCAAATA,GGACAAAAAAAACCAATTACATAGAAATTTCATCATATCAAATA]
TTTGAACACATGTATGAAACATTAAATGGACAAAAAAAACCAATTACATAGCTTATATGTAAATTGCAAGACTAATTTTTGAGCCTAATTACACCATGAT

Reverse complement sequence

ATCATGGTGTAATTAGGCTCAAAAATTAGTCTTGCAATTTACATATAAGCTATGTAATTGGTTTTTTTTGTCCATTTAATGTTTCATACATGTGTTCAAA[C/T,TATTTGATATGATGAAATTTCTATGTAATTGGTTTTTTTTATCC,TATTTGATATGATGAAATTTCTATGTAATTGGTTTTTTTTGTCC]
ATTTAATATGATGAATTTTTTTAAAGTTTGAAGTGAACTAAAGACTGCCCCTACTCCAATTCTTTTCCATGCGTTATGTACGGAATAATCAAAAGGGATT

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	48.20%	11.60%	14.85%	25.12%	GGATAAAAAAAACCAATTACATAGAAATTTCATCATATCAAATA: 0.15%; GGACAAAAAAAACCAATTACATAGAAATTTCATCATATCAAATA: 0.02%
All Indica	2759	61.20%	15.40%	15.19%	8.05%	GGATAAAAAAAACCAATTACATAGAAATTTCATCATATCAAATA: 0.07%; GGACAAAAAAAACCAATTACATAGAAATTTCATCATATCAAATA: 0.04%
All Japonica	1512	22.00%	4.40%	12.50%	61.18%	NA
Aus	269	69.50%	16.00%	10.04%	2.97%	GGATAAAAAAAACCAATTACATAGAAATTTCATCATATCAAATA: 1.49%
Indica I	595	20.20%	24.50%	44.20%	11.09%	NA
Indica II	465	89.20%	2.40%	1.51%	6.88%	NA
Indica III	913	65.00%	18.20%	8.65%	7.89%	GGATAAAAAAAACCAATTACATAGAAATTTCATCATATCAAATA: 0.22%; GGACAAAAAAAACCAATTACATAGAAATTTCATCATATCAAATA: 0.11%
Indica Intermediate	786	71.40%	13.10%	8.91%	6.62%	NA
Temperate Japonica	767	35.90%	3.40%	8.21%	52.54%	NA
Tropical Japonica	504	7.30%	5.20%	17.86%	69.64%	NA
Japonica Intermediate	241	8.30%	5.80%	14.94%	70.95%	NA
VI/Aromatic	96	21.90%	8.30%	55.21%	13.54%	GGATAAAAAAAACCAATTACATAGAAATTTCATCATATCAAATA: 1.04%
Intermediate	90	56.70%	6.70%	15.56%	21.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0623461786	G -> DEL	N	N	silent_mutation	Average:74.56; most accessible tissue: Callus, score: 87.64	N	N	N	N
vg0623461786	G -> GGATAAAAAAAACCAATTACATAGAAATTT CATCATATCAAATA	LOC_Os06g39510.1	downstream_gene_variant ; 4884.0bp to feature; MODIFIER	silent_mutation	Average:74.56; most accessible tissue: Callus, score: 87.64	N	N	N	N
vg0623461786	G -> GGATAAAAAAAACCAATTACATAGAAATTT CATCATATCAAATA	LOC_Os06g39515.1	intron_variant ; MODIFIER	silent_mutation	Average:74.56; most accessible tissue: Callus, score: 87.64	N	N	N	N
vg0623461786	G -> A	LOC_Os06g39510.1	downstream_gene_variant ; 4883.0bp to feature; MODIFIER	silent_mutation	Average:74.56; most accessible tissue: Callus, score: 87.64	N	N	N	N
vg0623461786	G -> A	LOC_Os06g39515.1	intron_variant ; MODIFIER	silent_mutation	Average:74.56; most accessible tissue: Callus, score: 87.64	N	N	N	N
vg0623461786	G -> GGACAAAAAAAACCAATTACATAGAAATTT CATCATATCAAATA	LOC_Os06g39510.1	downstream_gene_variant ; 4884.0bp to feature; MODIFIER	silent_mutation	Average:74.56; most accessible tissue: Callus, score: 87.64	N	N	N	N
vg0623461786	G -> GGACAAAAAAAACCAATTACATAGAAATTT CATCATATCAAATA	LOC_Os06g39515.1	intron_variant ; MODIFIER	silent_mutation	Average:74.56; most accessible tissue: Callus, score: 87.64	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0623461786	NA	6.45E-07	mr1229	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0623461786	NA	4.82E-10	mr1565	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0623461786	NA	6.01E-11	mr1659	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0623461786	9.66E-07	8.74E-10	mr1659	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0623461786	4.20E-08	7.34E-09	mr1766	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
vg0623461786	NA	2.56E-07	mr1659_2	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251