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Detailed information for vg0515214255:

Variant ID: vg0515214255 (JBrowse)	Variation Type: INDEL
Chromosome: chr05	Position: 15214255
Reference Allele: CATGTCAGTTACATAGTAGTTACAATTTAATTAT	Alternative Allele: C
Primary Allele: CATGTCAGTTACATAGTAGT TACAATTTAATTAT	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CAGCAGGATCGAACCCAACACCTACAACTTGGAGGTTTGTTCAACTAACCAGTTGCTCCATCATGCTTTTTTTAGCAACACTCGAGTTATATATCAGTTA[CATGTCAGTTACATAGTAGTTACAATTTAATTAT/C]
ATAGTAGTTACATTTGAAAGTTTTTCATCCAAAAACTGTCGACAGTTGTATAGCTACTCCCTACATATATATATATACACACGCAAAGGTATTAGGAAAA

Reverse complement sequence

TTTTCCTAATACCTTTGCGTGTGTATATATATATATGTAGGGAGTAGCTATACAACTGTCGACAGTTTTTGGATGAAAAACTTTCAAATGTAACTACTAT[ATAATTAAATTGTAACTACTATGTAACTGACATG/G]
TAACTGATATATAACTCGAGTGTTGCTAAAAAAAGCATGATGGAGCAACTGGTTAGTTGAACAAACCTCCAAGTTGTAGGTGTTGGGTTCGATCCTGCTG

Allele Frequencies:

Populations	Population Size	Frequency of CATGTCAGTTACATAGTAGT TACAATTTAATTAT(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	58.60%	0.10%	0.34%	40.92%	NA
All Indica	2759	44.30%	0.00%	0.47%	55.20%	NA
All Japonica	1512	77.50%	0.30%	0.13%	22.02%	NA
Aus	269	80.30%	0.00%	0.37%	19.33%	NA
Indica I	595	26.10%	0.00%	0.50%	73.45%	NA
Indica II	465	63.00%	0.00%	0.00%	36.99%	NA
Indica III	913	54.40%	0.00%	0.44%	45.13%	NA
Indica Intermediate	786	35.40%	0.00%	0.76%	63.87%	NA
Temperate Japonica	767	93.50%	0.70%	0.13%	5.74%	NA
Tropical Japonica	504	52.00%	0.00%	0.20%	47.82%	NA
Japonica Intermediate	241	80.10%	0.00%	0.00%	19.92%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	71.10%	0.00%	0.00%	28.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0515214255	CATGTCAGTTACATAGTAGTTACAATTTAATTAT -> DEL	N	N	silent_mutation	Average:20.529; most accessible tissue: Callus, score: 88.602	N	N	N	N
vg0515214255	CATGTCAGTTACATAGTAGTTACAATTTAATTAT -> C	LOC_Os05g26140.1	upstream_gene_variant ; 1826.0bp to feature; MODIFIER	silent_mutation	Average:20.529; most accessible tissue: Callus, score: 88.602	N	N	N	N
vg0515214255	CATGTCAGTTACATAGTAGTTACAATTTAATTAT -> C	LOC_Os05g26150.1	upstream_gene_variant ; 4104.0bp to feature; MODIFIER	silent_mutation	Average:20.529; most accessible tissue: Callus, score: 88.602	N	N	N	N
vg0515214255	CATGTCAGTTACATAGTAGTTACAATTTAATTAT -> C	LOC_Os05g26140-LOC_Os05g26150	intergenic_region ; MODIFIER	silent_mutation	Average:20.529; most accessible tissue: Callus, score: 88.602	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0515214255	NA	8.96E-06	mr1113	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
vg0515214255	2.19E-06	5.68E-08	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
vg0515214255	NA	2.31E-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
vg0515214255	8.32E-06	1.07E-07	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
vg0515214255	NA	3.82E-08	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
vg0515214255	NA	2.76E-06	mr1119	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
vg0515214255	5.59E-06	6.44E-09	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
vg0515214255	NA	5.84E-06	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
vg0515214255	8.19E-07	7.75E-10	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
vg0515214255	3.66E-06	3.16E-08	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
vg0515214255	NA	5.89E-09	mr1693	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
vg0515214255	NA	1.21E-06	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
vg0515214255	4.15E-06	2.81E-07	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
vg0515214255	9.72E-06	1.14E-07	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
vg0515214255	1.48E-06	4.38E-09	mr1118_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
vg0515214255	7.88E-06	1.16E-07	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
vg0515214255	NA	1.58E-06	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
vg0515214255	NA	1.32E-07	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
vg0515214255	7.29E-07	5.59E-09	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
vg0515214255	8.05E-06	3.02E-08	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
vg0515214255	NA	1.82E-06	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
vg0515214255	3.95E-08	2.98E-11	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