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Detailed information for vg1009643741:

Variant ID: vg1009643741 (JBrowse)	Variation Type: INDEL
Chromosome: chr10	Position: 9643741
Reference Allele: ACTTCCACGTGGATGGCTTAGATTCCTCCCCTATGGTGGTTGCAGGGTGTTTTGGT	Alternative Allele: GCTTCCACGTGGATGGCTTAGATTCCTCCCCTATGGTGGTTGCAGGGTGTTTTGGT,A
Primary Allele: ACTTCCACGTGGATGGCTTA GATTCCTCCCCTATGGTGGT TGCAGGGTGTTTTGGT	Secondary Allele: GCTTCCACGTGGATGGCTTA GATTCCTCCCCTATGGTGGT TGCAGGGTGTTTTGGT

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGGTTATTGGGGGCCCATTAAGCAACCTATCGGCCAAAAGAGAGGCCGGGAGGACACTTTTTGGGTTCGGCCGAACCCGTTCTGCGGCCGTTCACCGTCT[ACTTCCACGTGGATGGCTTAGATTCCTCCCCTATGGTGGTTGCAGGGTGTTTTGGT/GCTTCCACGTGGATGGCTTAGATTCCTCCCCTATGGTGGTTGCAGGGTGTTTTGGT,A]
CATTTCCCATGCCCCTAACCATCATTTGGAGCCTATATAAGGAGGTCTTCATCTCATTCCAACACACACAACTTAGAACGGAATTATAAGAGGCTCTATT

Reverse complement sequence

AATAGAGCCTCTTATAATTCCGTTCTAAGTTGTGTGTGTTGGAATGAGATGAAGACCTCCTTATATAGGCTCCAAATGATGGTTAGGGGCATGGGAAATG[ACCAAAACACCCTGCAACCACCATAGGGGAGGAATCTAAGCCATCCACGTGGAAGT/ACCAAAACACCCTGCAACCACCATAGGGGAGGAATCTAAGCCATCCACGTGGAAGC,T]
AGACGGTGAACGGCCGCAGAACGGGTTCGGCCGAACCCAAAAAGTGTCCTCCCGGCCTCTCTTTTGGCCGATAGGTTGCTTAATGGGCCCCCAATAACCT

Allele Frequencies:

Populations	Population Size	Frequency of ACTTCCACGTGGATGGCTTA GATTCCTCCCCTATGGTGGT TGCAGGGTGTTTTGGT(primary allele)	Frequency of GCTTCCACGTGGATGGCTTA GATTCCTCCCCTATGGTGGT TGCAGGGTGTTTTGGT(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	66.30%	1.80%	2.22%	28.82%	A: 0.89%
All Indica	2759	62.80%	0.70%	1.88%	34.54%	A: 0.14%
All Japonica	1512	67.80%	4.20%	2.25%	25.46%	A: 0.26%
Aus	269	89.20%	0.00%	2.23%	1.49%	A: 7.06%
Indica I	595	77.30%	0.00%	0.67%	22.02%	NA
Indica II	465	44.70%	0.40%	2.80%	52.04%	NA
Indica III	913	65.80%	1.50%	2.08%	30.56%	NA
Indica Intermediate	786	58.90%	0.30%	2.04%	38.30%	A: 0.51%
Temperate Japonica	767	72.90%	0.30%	0.65%	26.21%	NA
Tropical Japonica	504	51.80%	12.30%	5.16%	30.75%	NA
Japonica Intermediate	241	85.10%	0.00%	1.24%	12.03%	A: 1.66%
VI/Aromatic	96	81.20%	0.00%	6.25%	1.04%	A: 11.46%
Intermediate	90	65.60%	1.10%	7.78%	21.11%	A: 4.44%

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1009643741	ACTTCCACGTGGATGGCTTAGATTCCTCCCCTATGGTGGTTGCAGGGTGTTTTGGT -> GCTTCCACGTGGATGGCTTAGATTCCTCCC CTATGGTGGTTGCAGGGTGTTTTGGT	LOC_Os10g18940.1	downstream_gene_variant ; 30.0bp to feature; MODIFIER	silent_mutation	Average:40.086; most accessible tissue: Minghui63 flag leaf, score: 52.88	N	N	N	N
vg1009643741	ACTTCCACGTGGATGGCTTAGATTCCTCCCCTATGGTGGTTGCAGGGTGTTTTGGT -> GCTTCCACGTGGATGGCTTAGATTCCTCCC CTATGGTGGTTGCAGGGTGTTTTGGT	LOC_Os10g18930-LOC_Os10g18940	intergenic_region ; MODIFIER	silent_mutation	Average:40.086; most accessible tissue: Minghui63 flag leaf, score: 52.88	N	N	N	N
vg1009643741	ACTTCCACGTGGATGGCTTAGATTCCTCCCCTATGGTGGTTGCAGGGTGTTTTGGT -> A	LOC_Os10g18940.1	frameshift_variant&stop_lost&splice_region_variant ; p.Asp670fs; HIGH	frameshift_variant	Average:40.086; most accessible tissue: Minghui63 flag leaf, score: 52.88	N	N	N	N
vg1009643741	ACTTCCACGTGGATGGCTTAGATTCCTCCCCTATGGTGGTTGCAGGGTGTTTTGGT -> A	LOC_Os10g18940.1	downstream_gene_variant ; 29.0bp to feature; MODIFIER	frameshift_variant	Average:40.086; most accessible tissue: Minghui63 flag leaf, score: 52.88	N	N	N	N
vg1009643741	ACTTCCACGTGGATGGCTTAGATTCCTCCCCTATGGTGGTTGCAGGGTGTTTTGGT -> DEL	N	N	silent_mutation	Average:40.086; most accessible tissue: Minghui63 flag leaf, score: 52.88	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1009643741	8.37E-07	8.37E-07	mr1529	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