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Detailed information for vg0507120963:

Variant ID: vg0507120963 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 7120963
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GGCTGAATTCCAAGACTCGGATTCCTCGTCTCCCCTCTTTAACCTGAAACTAAGATGTGTTTCCTGCGACCCTTCTCAGAACCTGATTAGTTCCCACGCA[G/A]
AAACTTTTTATTCCGTCATATTAAATGTTTAGACACATGCATAGAGTATTAAATATAGAAAAAAACTAATCACGCTGATTGCGTGTAAATTGCGAGACGA

Reverse complement sequence

TCGTCTCGCAATTTACACGCAATCAGCGTGATTAGTTTTTTTCTATATTTAATACTCTATGCATGTGTCTAAACATTTAATATGACGGAATAAAAAGTTT[C/T]
TGCGTGGGAACTAATCAGGTTCTGAGAAGGGTCGCAGGAAACACATCTTAGTTTCAGGTTAAAGAGGGGAGACGAGGAATCCGAGTCTTGGAATTCAGCC

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	81.40%	18.60%	0.06%	0.00%	NA
All Indica	2759	99.50%	0.40%	0.11%	0.00%	NA
All Japonica	1512	43.90%	56.10%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.50%	0.30%	0.17%	0.00%	NA
Indica II	465	98.70%	1.30%	0.00%	0.00%	NA
Indica III	913	99.80%	0.20%	0.00%	0.00%	NA
Indica Intermediate	786	99.50%	0.30%	0.25%	0.00%	NA
Temperate Japonica	767	9.30%	90.70%	0.00%	0.00%	NA
Tropical Japonica	504	90.90%	9.10%	0.00%	0.00%	NA
Japonica Intermediate	241	56.00%	44.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	81.10%	18.90%	0.00%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0507120963	G -> A	LOC_Os05g12380.1	upstream_gene_variant ; 2907.0bp to feature; MODIFIER	silent_mutation	Average:54.093; most accessible tissue: Callus, score: 70.192	N	N	N	N
vg0507120963	G -> A	LOC_Os05g12370-LOC_Os05g12380	intergenic_region ; MODIFIER	silent_mutation	Average:54.093; most accessible tissue: Callus, score: 70.192	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0507120963	NA	4.49E-43	Grain_thickness	All	YES	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0507120963	NA	7.10E-14	Grain_thickness	Jap_All	Not	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0507120963	NA	1.86E-06	mr1401	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
vg0507120963	NA	6.25E-09	mr1549	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
vg0507120963	2.08E-07	1.67E-11	mr1593	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
vg0507120963	4.91E-10	6.50E-28	mr1593	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
vg0507120963	NA	4.34E-07	mr1723	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
vg0507120963	NA	2.91E-12	mr1741	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
vg0507120963	NA	1.92E-23	mr1862	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
vg0507120963	NA	1.07E-11	mr1879	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
vg0507120963	NA	8.95E-10	mr1093_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
vg0507120963	9.39E-09	3.18E-12	mr1593_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
vg0507120963	4.08E-15	4.77E-42	mr1593_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
vg0507120963	NA	1.35E-28	mr1789_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