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Detailed information for vg0915298743:

Variant ID: vg0915298743 (JBrowse)	Variation Type: INDEL
Chromosome: chr09	Position: 15298743
Reference Allele: A	Alternative Allele: AATAATTTGTGTT,AATAATTTGTGTTACT,AATAATCTGTGTTACT,G,AATAATCTGTGTTACTCCTCT,AATAAT
Primary Allele: A	Secondary Allele: AATAATTTGTGTTACT

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 76. )

Flanking Sequence (100 bp) in Reference Genome:

CTCCATCATGTTTACTCTGACTTTTGAGTGTAAGCAATCATTTAATTTTACATGATACAACCACGATCCAATCTTTATGTGCATGCATTTGTTTTTAGGG[A/AATAATTTGTGTT,AATAATTTGTGTTACT,AATAATCTGTGTTACT,G,AATAATCTGTGTTACTCCTCT,AATAAT]
CCGCCTATTCTGCAGTCGATTGCAATTTTTGCGTTTGGTCAGTCAACTTTATGCACCATTAGATATGTATCTAACGGTAAAGCTCAAAAAATCAAAACGT

Reverse complement sequence

ACGTTTTGATTTTTTGAGCTTTACCGTTAGATACATATCTAATGGTGCATAAAGTTGACTGACCAAACGCAAAAATTGCAATCGACTGCAGAATAGGCGG[T/AACACAAATTATT,AGTAACACAAATTATT,AGTAACACAGATTATT,C,AGAGGAGTAACACAGATTATT,ATTATT]
CCCTAAAAACAAATGCATGCACATAAAGATTGGATCGTGGTTGTATCATGTAAAATTAAATGATTGCTTACACTCAAAAGTCAGAGTAAACATGATGGAG

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of AATAATTTGTGTTACT(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	33.50%	5.70%	23.23%	32.63%	G: 2.79%; AATAATTTGTGTT: 1.48%; AATAATCTGTGTTACT: 0.44%; AATAAT: 0.19%; AATAATCTGTGTTACTCCTCT: 0.08%
All Indica	2759	2.50%	8.30%	32.84%	53.03%	AATAATTTGTGTT: 2.17%; AATAATCTGTGTTACT: 0.69%; AATAAT: 0.33%; AATAATCTGTGTTACTCCTCT: 0.14%
All Japonica	1512	89.40%	0.10%	1.46%	0.40%	G: 8.60%; AATAATCTGTGTTACT: 0.07%
Aus	269	2.60%	12.60%	57.99%	23.42%	AATAATTTGTGTT: 3.35%
Indica I	595	1.00%	3.00%	28.74%	64.87%	AATAATTTGTGTT: 1.01%; AATAATCTGTGTTACT: 0.50%; AATAAT: 0.50%; AATAATCTGTGTTACTCCTCT: 0.34%
Indica II	465	5.20%	4.30%	23.87%	64.30%	AATAATTTGTGTT: 1.72%; AATAATCTGTGTTACT: 0.22%; AATAATCTGTGTTACTCCTCT: 0.22%; AATAAT: 0.22%
Indica III	913	1.20%	15.20%	38.88%	40.42%	AATAATTTGTGTT: 2.85%; AATAATCTGTGTTACT: 1.10%; AATAAT: 0.22%; AATAATCTGTGTTACTCCTCT: 0.11%
Indica Intermediate	786	3.40%	6.70%	34.22%	52.04%	AATAATTTGTGTT: 2.54%; AATAATCTGTGTTACT: 0.64%; AATAAT: 0.38%
Temperate Japonica	767	95.00%	0.10%	1.04%	0.26%	G: 3.39%; AATAATCTGTGTTACT: 0.13%
Tropical Japonica	504	94.00%	0.20%	0.40%	0.40%	G: 4.96%
Japonica Intermediate	241	61.40%	0.00%	4.98%	0.83%	G: 32.78%
VI/Aromatic	96	96.90%	0.00%	0.00%	2.08%	G: 1.04%
Intermediate	90	70.00%	2.20%	15.56%	8.89%	AATAATCTGTGTTACT: 1.11%; AATAATTTGTGTT: 1.11%; G: 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
vg0915298743	A -> DEL	N	N	silent_mutation	Average:27.179; most accessible tissue: Minghui63 root, score: 47.894	N	N	N	N
vg0915298743	A -> G	LOC_Os09g25510.1	upstream_gene_variant ; 1262.0bp to feature; MODIFIER	silent_mutation	Average:27.179; most accessible tissue: Minghui63 root, score: 47.894	N	N	N	N
vg0915298743	A -> G	LOC_Os09g25500-LOC_Os09g25510	intergenic_region ; MODIFIER	silent_mutation	Average:27.179; most accessible tissue: Minghui63 root, score: 47.894	N	N	N	N
vg0915298743	A -> AATAATTTGTGTT	LOC_Os09g25510.1	upstream_gene_variant ; 1261.0bp to feature; MODIFIER	silent_mutation	Average:27.179; most accessible tissue: Minghui63 root, score: 47.894	N	N	N	N
vg0915298743	A -> AATAATTTGTGTT	LOC_Os09g25500-LOC_Os09g25510	intergenic_region ; MODIFIER	silent_mutation	Average:27.179; most accessible tissue: Minghui63 root, score: 47.894	N	N	N	N
vg0915298743	A -> AATAAT	LOC_Os09g25510.1	upstream_gene_variant ; 1261.0bp to feature; MODIFIER	silent_mutation	Average:27.179; most accessible tissue: Minghui63 root, score: 47.894	N	N	N	N
vg0915298743	A -> AATAAT	LOC_Os09g25500-LOC_Os09g25510	intergenic_region ; MODIFIER	silent_mutation	Average:27.179; most accessible tissue: Minghui63 root, score: 47.894	N	N	N	N
vg0915298743	A -> AATAATTTGTGTTACT	LOC_Os09g25510.1	upstream_gene_variant ; 1261.0bp to feature; MODIFIER	silent_mutation	Average:27.179; most accessible tissue: Minghui63 root, score: 47.894	N	N	N	N
vg0915298743	A -> AATAATTTGTGTTACT	LOC_Os09g25500-LOC_Os09g25510	intergenic_region ; MODIFIER	silent_mutation	Average:27.179; most accessible tissue: Minghui63 root, score: 47.894	N	N	N	N
vg0915298743	A -> AATAATCTGTGTTACT	LOC_Os09g25510.1	upstream_gene_variant ; 1261.0bp to feature; MODIFIER	silent_mutation	Average:27.179; most accessible tissue: Minghui63 root, score: 47.894	N	N	N	N
vg0915298743	A -> AATAATCTGTGTTACT	LOC_Os09g25500-LOC_Os09g25510	intergenic_region ; MODIFIER	silent_mutation	Average:27.179; most accessible tissue: Minghui63 root, score: 47.894	N	N	N	N
vg0915298743	A -> AATAATCTGTGTTACTCCTCT	LOC_Os09g25510.1	upstream_gene_variant ; 1261.0bp to feature; MODIFIER	silent_mutation	Average:27.179; most accessible tissue: Minghui63 root, score: 47.894	N	N	N	N
vg0915298743	A -> AATAATCTGTGTTACTCCTCT	LOC_Os09g25500-LOC_Os09g25510	intergenic_region ; MODIFIER	silent_mutation	Average:27.179; most accessible tissue: Minghui63 root, score: 47.894	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0915298743	6.43E-08	3.81E-10	mr1113	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
vg0915298743	NA	9.22E-09	mr1114	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
vg0915298743	NA	3.79E-06	mr1116	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
vg0915298743	4.95E-07	3.04E-12	mr1117	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
vg0915298743	NA	1.35E-10	mr1118	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
vg0915298743	2.88E-07	1.69E-10	mr1119	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
vg0915298743	NA	3.68E-06	mr1120	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
vg0915298743	2.24E-06	1.93E-10	mr1123	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
vg0915298743	NA	8.16E-06	mr1180	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
vg0915298743	NA	1.61E-09	mr1240	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
vg0915298743	NA	1.58E-09	mr1242	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
vg0915298743	1.80E-06	7.18E-10	mr1247	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
vg0915298743	NA	1.82E-07	mr1495	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
vg0915298743	1.87E-07	9.96E-13	mr1496	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
vg0915298743	1.16E-06	2.00E-09	mr1917	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
vg0915298743	NA	5.36E-07	mr1936	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
vg0915298743	NA	5.27E-09	mr1961	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
vg0915298743	1.62E-06	1.93E-11	mr1113_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
vg0915298743	NA	9.42E-09	mr1114_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
vg0915298743	3.70E-06	4.19E-11	mr1117_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
vg0915298743	NA	4.29E-10	mr1118_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
vg0915298743	3.43E-06	3.72E-11	mr1119_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
vg0915298743	NA	6.57E-09	mr1120_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
vg0915298743	NA	5.75E-09	mr1123_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
vg0915298743	NA	3.35E-08	mr1180_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
vg0915298743	NA	1.30E-07	mr1183_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
vg0915298743	2.84E-06	2.32E-12	mr1240_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
vg0915298743	NA	4.18E-09	mr1242_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
vg0915298743	NA	5.42E-09	mr1247_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
vg0915298743	NA	2.59E-08	mr1495_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
vg0915298743	1.07E-06	2.28E-12	mr1496_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
vg0915298743	NA	1.02E-06	mr1936_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
vg0915298743	NA	3.86E-06	mr1961_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