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Detailed information for vg1019412004:

Variant ID: vg1019412004 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 19412004
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 177. )

Flanking Sequence (100 bp) in Reference Genome:

TTGTAAACACAATACCACCCCTCCTATAAACAGACTGGGGCAAGGCCAATCGTAAAAACCACTAATCAAACGTTAAAATCAATCAACTACCCCTACCCTT[G/A]
TATTCTACATCTCCCTTCTTCTACTAGCTACCTGTATCTCACGTCATTTCATCCTCAACCCCCTAATTGCTCGTTGTCTCTCTCACTGCTGGAGAAAGGG

Reverse complement sequence

CCCTTTCTCCAGCAGTGAGAGAGACAACGAGCAATTAGGGGGTTGAGGATGAAATGACGTGAGATACAGGTAGCTAGTAGAAGAAGGGAGATGTAGAATA[C/T]
AAGGGTAGGGGTAGTTGATTGATTTTAACGTTTGATTAGTGGTTTTTACGATTGGCCTTGCCCCAGTCTGTTTATAGGAGGGGTGGTATTGTGTTTACAA

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	12.00%	11.70%	1.78%	74.52%	NA
All Indica	2759	0.50%	0.80%	0.33%	98.30%	NA
All Japonica	1512	33.50%	34.60%	4.63%	27.31%	NA
Aus	269	1.10%	0.00%	0.37%	98.51%	NA
Indica I	595	0.00%	2.20%	0.34%	97.48%	NA
Indica II	465	0.20%	1.10%	0.43%	98.28%	NA
Indica III	913	0.50%	0.20%	0.11%	99.12%	NA
Indica Intermediate	786	1.10%	0.40%	0.51%	97.96%	NA
Temperate Japonica	767	27.80%	60.80%	6.78%	4.69%	NA
Tropical Japonica	504	29.80%	1.60%	1.19%	67.46%	NA
Japonica Intermediate	241	59.30%	20.30%	4.98%	15.35%	NA
VI/Aromatic	96	27.10%	0.00%	0.00%	72.92%	NA
Intermediate	90	18.90%	7.80%	4.44%	68.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1019412004	G -> A	LOC_Os10g36310.1	upstream_gene_variant ; 2741.0bp to feature; MODIFIER	silent_mutation	Average:15.128; most accessible tissue: Callus, score: 92.381	N	N	N	N
vg1019412004	G -> A	LOC_Os10g36320.1	upstream_gene_variant ; 1591.0bp to feature; MODIFIER	silent_mutation	Average:15.128; most accessible tissue: Callus, score: 92.381	N	N	N	N
vg1019412004	G -> A	LOC_Os10g36340.2	upstream_gene_variant ; 1265.0bp to feature; MODIFIER	silent_mutation	Average:15.128; most accessible tissue: Callus, score: 92.381	N	N	N	N
vg1019412004	G -> A	LOC_Os10g36350.1	downstream_gene_variant ; 3556.0bp to feature; MODIFIER	silent_mutation	Average:15.128; most accessible tissue: Callus, score: 92.381	N	N	N	N
vg1019412004	G -> A	LOC_Os10g36350.2	downstream_gene_variant ; 3599.0bp to feature; MODIFIER	silent_mutation	Average:15.128; most accessible tissue: Callus, score: 92.381	N	N	N	N
vg1019412004	G -> A	LOC_Os10g36320-LOC_Os10g36340	intergenic_region ; MODIFIER	silent_mutation	Average:15.128; most accessible tissue: Callus, score: 92.381	N	N	N	N
vg1019412004	G -> DEL	N	N	silent_mutation	Average:15.128; most accessible tissue: Callus, score: 92.381	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1019412004	1.91E-07	1.23E-14	Spikelet_length	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
vg1019412004	6.56E-06	NA	Spikelet_length	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
vg1019412004	NA	6.32E-06	mr1509_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
vg1019412004	NA	9.00E-06	mr1577_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