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Detailed information for vg1107881424:

Variant ID: vg1107881424 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 7881424
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GTCAGCTCTTAATAATCTGGGCTGAAAAACCTAGTTTCTAACTAATAGTATCTAAATTCTACGGCTACACATTCTAAAATTCTGAGTGAAATCCTGGACT[G/A]
TTTAGGGGAGCTTCTGGCAGCTGGAGATTCTTAGATAAGCTGCAACCGTCAGAAACTCCCTTGATAGACTCCTAGAACCTATCAGAGGGGACTTTTAGCA

Reverse complement sequence

TGCTAAAAGTCCCCTCTGATAGGTTCTAGGAGTCTATCAAGGGAGTTTCTGACGGTTGCAGCTTATCTAAGAATCTCCAGCTGCCAGAAGCTCCCCTAAA[C/T]
AGTCCAGGATTTCACTCAGAATTTTAGAATGTGTAGCCGTAGAATTTAGATACTATTAGTTAGAAACTAGGTTTTTCAGCCCAGATTATTAAGAGCTGAC

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	64.70%	19.20%	13.42%	2.75%	NA
All Indica	2759	71.60%	2.70%	21.20%	4.46%	NA
All Japonica	1512	56.00%	42.60%	1.19%	0.20%	NA
Aus	269	39.00%	53.90%	7.06%	0.00%	NA
Indica I	595	88.60%	0.80%	8.91%	1.68%	NA
Indica II	465	61.10%	0.40%	33.55%	4.95%	NA
Indica III	913	72.10%	1.80%	19.82%	6.35%	NA
Indica Intermediate	786	64.50%	6.60%	24.81%	4.07%	NA
Temperate Japonica	767	84.40%	14.90%	0.78%	0.00%	NA
Tropical Japonica	504	20.00%	79.20%	0.79%	0.00%	NA
Japonica Intermediate	241	41.10%	54.40%	3.32%	1.24%	NA
VI/Aromatic	96	79.20%	19.80%	1.04%	0.00%	NA
Intermediate	90	57.80%	25.60%	12.22%	4.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1107881424	G -> A	LOC_Os11g14140.1	upstream_gene_variant ; 1876.0bp to feature; MODIFIER	silent_mutation	Average:75.877; most accessible tissue: Zhenshan97 root, score: 88.397	N	N	N	N
vg1107881424	G -> A	LOC_Os11g14140-LOC_Os11g14150	intergenic_region ; MODIFIER	silent_mutation	Average:75.877; most accessible tissue: Zhenshan97 root, score: 88.397	N	N	N	N
vg1107881424	G -> DEL	N	N	silent_mutation	Average:75.877; most accessible tissue: Zhenshan97 root, score: 88.397	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1107881424	NA	6.85E-06	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
vg1107881424	NA	1.07E-06	mr1408	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
vg1107881424	NA	1.58E-07	mr1042_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
vg1107881424	NA	2.45E-07	mr1064_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
vg1107881424	NA	8.80E-06	mr1269_2	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
vg1107881424	NA	5.19E-06	mr1295_2	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
vg1107881424	NA	2.10E-09	mr1502_2	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
vg1107881424	NA	1.28E-07	mr1502_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
vg1107881424	NA	4.12E-11	mr1543_2	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
vg1107881424	NA	4.20E-09	mr1543_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
vg1107881424	NA	2.07E-12	mr1680_2	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
vg1107881424	NA	3.86E-06	mr1704_2	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
vg1107881424	NA	1.85E-15	mr1742_2	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
vg1107881424	1.42E-06	1.42E-06	mr1777_2	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
vg1107881424	NA	5.80E-09	mr1871_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