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Detailed information for vg0906785691:

Variant ID: vg0906785691 (JBrowse)	Variation Type: INDEL
Chromosome: chr09	Position: 6785691
Reference Allele: T	Alternative Allele: C,TCTGATCGC,G,A,TCTGACCGC,TTCTGGCC
Primary Allele: T	Secondary Allele: TCTGATCGC

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCTCATGATGTGCCAATACCTACTGGAGATGGAGTTGAAGTGTCCCCGAACAGAAAATCTGAAGCTGGTACCAGCTCCTCGTAGTCGGCCGGTCTGACCG[T/C,TCTGATCGC,G,A,TCTGACCGC,TTCTGGCC]
GGTCATGCGGCCGGTCTGACCGGGCCATCAGGCCTGTCTGACCGCCGACCCGATAGCGGTCCGACCAACACCTCAGGCCGGTCTGACCGTGCGCCAAATG

Reverse complement sequence

CATTTGGCGCACGGTCAGACCGGCCTGAGGTGTTGGTCGGACCGCTATCGGGTCGGCGGTCAGACAGGCCTGATGGCCCGGTCAGACCGGCCGCATGACC[A/G,GCGATCAGA,C,T,GCGGTCAGA,GGCCAGAA]
CGGTCAGACCGGCCGACTACGAGGAGCTGGTACCAGCTTCAGATTTTCTGTTCGGGGACACTTCAACTCCATCTCCAGTAGGTATTGGCACATCATGAGA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of TCTGATCGC(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	56.70%	9.80%	15.11%	10.92%	C: 7.30%; G: 0.11%; TCTGACCGC: 0.06%
All Indica	2759	61.00%	1.40%	20.70%	15.77%	C: 1.01%; G: 0.11%
All Japonica	1512	41.40%	26.90%	7.87%	4.96%	C: 18.72%; G: 0.13%; TCTGACCGC: 0.07%
Aus	269	94.10%	0.00%	1.86%	0.37%	C: 3.72%
Indica I	595	70.60%	0.00%	19.16%	9.08%	C: 1.01%; G: 0.17%
Indica II	465	76.30%	5.20%	7.10%	10.97%	C: 0.43%
Indica III	913	39.80%	0.30%	33.30%	25.19%	C: 1.42%
Indica Intermediate	786	69.50%	1.40%	15.27%	12.72%	C: 0.89%; G: 0.25%
Temperate Japonica	767	57.60%	8.10%	7.43%	0.91%	C: 25.81%; TCTGACCGC: 0.13%
Tropical Japonica	504	12.90%	58.90%	7.74%	10.52%	C: 9.72%; G: 0.20%
Japonica Intermediate	241	49.40%	19.50%	9.54%	6.22%	C: 14.94%; G: 0.41%
VI/Aromatic	96	65.60%	3.10%	8.33%	0.00%	C: 21.88%; TCTGACCGC: 1.04%
Intermediate	90	62.20%	15.60%	12.22%	5.56%	C: 3.33%; TCTGACCGC: 1.11%

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0906785691	T -> DEL	N	N	silent_mutation	Average:49.499; most accessible tissue: Minghui63 flag leaf, score: 71.116	N	N	N	N
vg0906785691	T -> G	LOC_Os09g12020-LOC_Os09g12050	intergenic_region ; MODIFIER	silent_mutation	Average:49.499; most accessible tissue: Minghui63 flag leaf, score: 71.116	N	N	N	N
vg0906785691	T -> TCTGATCGC	LOC_Os09g12020-LOC_Os09g12050	intergenic_region ; MODIFIER	silent_mutation	Average:49.499; most accessible tissue: Minghui63 flag leaf, score: 71.116	N	N	N	N
vg0906785691	T -> C	LOC_Os09g12020-LOC_Os09g12050	intergenic_region ; MODIFIER	silent_mutation	Average:49.499; most accessible tissue: Minghui63 flag leaf, score: 71.116	N	N	N	N
vg0906785691	T -> TTCTGGCC	LOC_Os09g12020-LOC_Os09g12050	intergenic_region ; MODIFIER	N	Average:49.499; most accessible tissue: Minghui63 flag leaf, score: 71.116	N	N	N	N
vg0906785691	T -> A	LOC_Os09g12020-LOC_Os09g12050	intergenic_region ; MODIFIER	N	Average:49.499; most accessible tissue: Minghui63 flag leaf, score: 71.116	N	N	N	N
vg0906785691	T -> TCTGACCGC	LOC_Os09g12020-LOC_Os09g12050	intergenic_region ; MODIFIER	silent_mutation	Average:49.499; most accessible tissue: Minghui63 flag leaf, score: 71.116	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0906785691	NA	3.78E-06	mr1002	Jap_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
vg0906785691	1.47E-07	1.02E-08	mr1991	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
vg0906785691	NA	1.49E-06	mr1330_2	Jap_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