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Detailed information for vg1107392564:

Variant ID: vg1107392564 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 7392564
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GAGCGTGAGAGATATATAGAAGAGATAGAAGAGAGAGAGAAACTGATAGGTGGGGCCCACTTATTTTTTAATAAATAAATTGCTGATTGGACTACCACGT[A/G]
GACCAAAACCACCGCAGATTAGATCGAGGGTGGTAATTCGTCCGGTTTACATAGTTGGGGGTGAAGAATGTCTGATTTTTTATGGTATTGGGGGTAATTC

Reverse complement sequence

GAATTACCCCCAATACCATAAAAAATCAGACATTCTTCACCCCCAACTATGTAAACCGGACGAATTACCACCCTCGATCTAATCTGCGGTGGTTTTGGTC[T/C]
ACGTGGTAGTCCAATCAGCAATTTATTTATTAAAAAATAAGTGGGCCCCACCTATCAGTTTCTCTCTCTCTTCTATCTCTTCTATATATCTCTCACGCTC

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	61.80%	4.10%	0.91%	33.20%	NA
All Indica	2759	50.20%	0.10%	0.62%	49.04%	NA
All Japonica	1512	79.90%	12.00%	0.93%	7.14%	NA
Aus	269	66.50%	0.40%	3.72%	29.37%	NA
Indica I	595	27.60%	0.20%	0.84%	71.43%	NA
Indica II	465	69.20%	0.00%	0.22%	30.54%	NA
Indica III	913	56.10%	0.20%	0.44%	43.26%	NA
Indica Intermediate	786	49.40%	0.00%	0.89%	49.75%	NA
Temperate Japonica	767	95.40%	0.70%	1.04%	2.87%	NA
Tropical Japonica	504	56.20%	34.10%	0.99%	8.73%	NA
Japonica Intermediate	241	80.10%	2.10%	0.41%	17.43%	NA
VI/Aromatic	96	97.90%	0.00%	0.00%	2.08%	NA
Intermediate	90	57.80%	10.00%	2.22%	30.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1107392564	A -> DEL	N	N	silent_mutation	Average:52.579; most accessible tissue: Minghui63 root, score: 89.072	N	N	N	N
vg1107392564	A -> G	LOC_Os11g13490.1	intron_variant ; MODIFIER	silent_mutation	Average:52.579; most accessible tissue: Minghui63 root, score: 89.072	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1107392564	3.44E-07	2.57E-09	mr1076	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
vg1107392564	NA	6.81E-08	mr1082	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
vg1107392564	6.30E-06	2.17E-08	mr1083	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
vg1107392564	2.17E-06	2.17E-06	mr1085	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
vg1107392564	NA	1.04E-06	mr1103	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
vg1107392564	NA	5.71E-06	mr1107	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
vg1107392564	1.46E-06	1.46E-06	mr1204	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
vg1107392564	1.68E-07	4.39E-09	mr1226	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
vg1107392564	NA	7.65E-06	mr1227	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
vg1107392564	2.09E-07	1.23E-08	mr1411	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
vg1107392564	NA	1.53E-06	mr1560	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
vg1107392564	3.61E-06	3.60E-06	mr1076_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
vg1107392564	NA	8.05E-07	mr1082_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
vg1107392564	NA	3.13E-07	mr1226_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