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Detailed information for vg0624862159:

Variant ID: vg0624862159 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 24862159
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 241. )

Flanking Sequence (100 bp) in Reference Genome:

TCGCAGCACCTTAAGCCTTGCGGTGATCCTAGAGTCGCCAACCACCTCGATCTAGCAAAGAGCTAAACCTAGATGGGTTTTGATAACTAAACCGGCTAGC[A/G]
GAGCCGATTTCTAGATAACTACCCGTCTCGTGGGCAAAACAGAAAGTTTTCAGGACAAACCTACAAAGAGGTGTCGCACTCTCGCAGCGGCGGCGGACGG

Reverse complement sequence

CCGTCCGCCGCCGCTGCGAGAGTGCGACACCTCTTTGTAGGTTTGTCCTGAAAACTTTCTGTTTTGCCCACGAGACGGGTAGTTATCTAGAAATCGGCTC[T/C]
GCTAGCCGGTTTAGTTATCAAAACCCATCTAGGTTTAGCTCTTTGCTAGATCGAGGTGGTTGGCGACTCTAGGATCACCGCAAGGCTTAAGGTGCTGCGA

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	88.90%	9.60%	0.21%	1.31%	NA
All Indica	2759	98.90%	0.90%	0.18%	0.00%	NA
All Japonica	1512	67.80%	27.80%	0.33%	4.03%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.80%	0.00%	0.17%	0.00%	NA
Indica II	465	98.90%	0.90%	0.22%	0.00%	NA
Indica III	913	98.60%	1.20%	0.22%	0.00%	NA
Indica Intermediate	786	98.70%	1.10%	0.13%	0.00%	NA
Temperate Japonica	767	54.90%	44.70%	0.39%	0.00%	NA
Tropical Japonica	504	81.90%	6.00%	0.00%	12.10%	NA
Japonica Intermediate	241	79.30%	19.90%	0.83%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	90.00%	8.90%	0.00%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0624862159	A -> G	LOC_Os06g41480.1	upstream_gene_variant ; 4738.0bp to feature; MODIFIER	silent_mutation	Average:53.257; most accessible tissue: Minghui63 young leaf, score: 71.254	N	N	N	N
vg0624862159	A -> G	LOC_Os06g41470.1	downstream_gene_variant ; 2395.0bp to feature; MODIFIER	silent_mutation	Average:53.257; most accessible tissue: Minghui63 young leaf, score: 71.254	N	N	N	N
vg0624862159	A -> G	LOC_Os06g41470-LOC_Os06g41480	intergenic_region ; MODIFIER	silent_mutation	Average:53.257; most accessible tissue: Minghui63 young leaf, score: 71.254	N	N	N	N
vg0624862159	A -> DEL	N	N	silent_mutation	Average:53.257; most accessible tissue: Minghui63 young leaf, score: 71.254	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0624862159	NA	5.90E-06	mr1763	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
vg0624862159	NA	5.10E-08	mr1880	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
vg0624862159	5.94E-07	NA	mr1070_2	Ind_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
vg0624862159	9.73E-07	NA	mr1076_2	Ind_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
vg0624862159	8.35E-06	NA	mr1103_2	Ind_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
vg0624862159	4.38E-06	NA	mr1120_2	Ind_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
vg0624862159	5.58E-06	NA	mr1123_2	Ind_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
vg0624862159	1.83E-06	1.55E-06	mr1227_2	Ind_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
vg0624862159	NA	1.35E-06	mr1229_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
vg0624862159	8.42E-06	NA	mr1241_2	Ind_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
vg0624862159	6.11E-06	NA	mr1247_2	Ind_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
vg0624862159	7.13E-06	1.44E-06	mr1264_2	Ind_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
vg0624862159	1.46E-06	NA	mr1437_2	Ind_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
vg0624862159	NA	1.18E-07	mr1880_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
vg0624862159	1.66E-06	NA	mr1949_2	Ind_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