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Detailed information for vg1215978234:

Variant ID: vg1215978234 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 15978234
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 113. )

Flanking Sequence (100 bp) in Reference Genome:

ATAATTAGTTGTATTGGTATAAATTTGATAGTACCGGCCAGCCAATCCTGACGGATAACTTCTTCTGGGATGGAATATGTTCTGGTCCACCTCTTTTGCG[G/A]
TAGTACTTGTGTGCTCTGTTTGAAGGAAACAATTGTTTTATTAGTAGTTAGAAGACTGGTGATCGACCTAAACAATTTATAGTAATGAAATGTTTATCAC

Reverse complement sequence

GTGATAAACATTTCATTACTATAAATTGTTTAGGTCGATCACCAGTCTTCTAACTACTAATAAAACAATTGTTTCCTTCAAACAGAGCACACAAGTACTA[C/T]
CGCAAAAGAGGTGGACCAGAACATATTCCATCCCAGAAGAAGTTATCCGTCAGGATTGGCTGGCCGGTACTATCAAATTTATACCAATACAACTAATTAT

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	17.50%	5.20%	16.72%	60.56%	NA
All Indica	2759	3.20%	0.40%	15.40%	81.08%	NA
All Japonica	1512	47.00%	12.00%	18.72%	22.35%	NA
Aus	269	2.20%	6.70%	21.56%	69.52%	NA
Indica I	595	0.80%	0.30%	2.52%	96.30%	NA
Indica II	465	3.90%	0.20%	38.49%	57.42%	NA
Indica III	913	2.40%	0.20%	12.81%	84.56%	NA
Indica Intermediate	786	5.30%	0.60%	14.50%	79.52%	NA
Temperate Japonica	767	81.20%	6.90%	7.69%	4.17%	NA
Tropical Japonica	504	1.80%	9.70%	37.70%	50.79%	NA
Japonica Intermediate	241	32.40%	32.80%	14.11%	20.75%	NA
VI/Aromatic	96	2.10%	28.10%	4.17%	65.62%	NA
Intermediate	90	23.30%	13.30%	22.22%	41.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1215978234	G -> DEL	LOC_Os12g27230.1	N	frameshift_variant	Average:10.145; most accessible tissue: Callus, score: 29.238	N	N	N	N
vg1215978234	G -> A	LOC_Os12g27230.1	synonymous_variant ; p.Tyr635Tyr; LOW	synonymous_codon	Average:10.145; most accessible tissue: Callus, score: 29.238	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1215978234	7.71E-07	NA	mr1017	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
vg1215978234	7.26E-06	NA	mr1019	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
vg1215978234	4.49E-09	NA	mr1022	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
vg1215978234	2.47E-09	NA	mr1023	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
vg1215978234	4.69E-07	NA	mr1055	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
vg1215978234	3.93E-10	NA	mr1079	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
vg1215978234	5.00E-06	NA	mr1132	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
vg1215978234	1.86E-11	NA	mr1142	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
vg1215978234	NA	8.10E-07	mr1280	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
vg1215978234	4.80E-11	NA	mr1489	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
vg1215978234	6.57E-10	NA	mr1491	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
vg1215978234	1.55E-08	NA	mr1778	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
vg1215978234	NA	9.36E-06	mr1788	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
vg1215978234	2.50E-06	NA	mr1023_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
vg1215978234	NA	3.42E-06	mr1051_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
vg1215978234	1.72E-06	NA	mr1079_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
vg1215978234	NA	1.15E-06	mr1318_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
vg1215978234	1.82E-07	NA	mr1489_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
vg1215978234	NA	7.88E-06	mr1728_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
vg1215978234	5.25E-06	5.25E-06	mr1777_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
vg1215978234	NA	1.86E-06	mr1788_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