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Detailed information for vg1006197978:

Variant ID: vg1006197978 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 6197978
Reference Allele: G	Alternative Allele: A
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:

GCAAGATTGAACTTTTGGCACAACTTCAAGAATGCAACGCCGAGTTGGATATAGAACATAAAAAGCTAGCCGATCTCCCAAAATCTGTTGAAGAGCAGAA[G/A]
GCAAGGCTAAAATCGGCTATCAAGAATGTTGCTGATCTGACCAAGTCTTTAAAAGTTATCCCTGGAACCGATGCTCAAGATGCCCAACCATTGAAGAAGT

Reverse complement sequence

ACTTCTTCAATGGTTGGGCATCTTGAGCATCGGTTCCAGGGATAACTTTTAAAGACTTGGTCAGATCAGCAACATTCTTGATAGCCGATTTTAGCCTTGC[C/T]
TTCTGCTCTTCAACAGATTTTGGGAGATCGGCTAGCTTTTTATGTTCTATATCCAACTCGGCGTTGCATTCTTGAAGTTGTGCCAAAAGTTCAATCTTGC

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	94.10%	1.20%	2.14%	2.62%	NA
All Indica	2759	94.90%	2.00%	3.15%	0.00%	NA
All Japonica	1512	91.30%	0.00%	0.66%	8.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	82.50%	6.70%	10.76%	0.00%	NA
Indica II	465	99.40%	0.40%	0.22%	0.00%	NA
Indica III	913	99.80%	0.10%	0.11%	0.00%	NA
Indica Intermediate	786	95.80%	1.50%	2.67%	0.00%	NA
Temperate Japonica	767	84.50%	0.00%	0.65%	14.86%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	95.00%	0.00%	2.07%	2.90%	NA
VI/Aromatic	96	97.90%	0.00%	0.00%	2.08%	NA
Intermediate	90	94.40%	0.00%	4.44%	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
vg1006197978	G -> A	LOC_Os10g11180.1	synonymous_variant ; p.Lys856Lys; LOW	synonymous_codon	Average:32.972; most accessible tissue: Zhenshan97 young leaf, score: 47.311	N	N	N	N
vg1006197978	G -> DEL	LOC_Os10g11180.1	N	frameshift_variant	Average:32.972; most accessible tissue: Zhenshan97 young leaf, score: 47.311	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1006197978	3.92E-08	1.45E-09	mr1053	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
vg1006197978	2.92E-09	6.59E-12	mr1070	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
vg1006197978	5.86E-06	3.46E-06	mr1076	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
vg1006197978	1.20E-12	2.15E-14	mr1128	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
vg1006197978	8.51E-06	NA	mr1139	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
vg1006197978	2.46E-07	1.55E-07	mr1147	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
vg1006197978	NA	7.39E-08	mr1180	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
vg1006197978	NA	2.71E-07	mr1183	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
vg1006197978	4.82E-06	NA	mr1204	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
vg1006197978	NA	3.83E-06	mr1211	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
vg1006197978	3.25E-06	NA	mr1436	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
vg1006197978	2.01E-06	NA	mr1437	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
vg1006197978	NA	2.14E-07	mr1503	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
vg1006197978	NA	7.70E-06	mr1963	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
vg1006197978	4.15E-07	1.11E-10	mr1053_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
vg1006197978	5.19E-09	1.89E-13	mr1128_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
vg1006197978	2.77E-06	4.61E-09	mr1147_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
vg1006197978	NA	3.67E-08	mr1180_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
vg1006197978	NA	4.29E-08	mr1183_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
vg1006197978	NA	6.19E-09	mr1204_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
vg1006197978	2.91E-07	2.91E-07	mr1250_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
vg1006197978	NA	1.36E-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