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Detailed information for vg1215654794:

Variant ID: vg1215654794 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 15654794
Reference Allele: C	Alternative Allele: T,G
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 27. )

Flanking Sequence (100 bp) in Reference Genome:

AGTTAGATTTGATTCAGTGCACCGAGCAGGAGAAGGTTTCTTTTGCTTCGCACCATTTGCATGGTCCTGCTGCTGAGTGGTGGGATCACTTTCGTCAAAA[C/T,G]
AGAGCTGCGGGAGAGCCTATCACTTGGCAGGAGTTTACTGCTGCTTTCAAGAAGACACATATACCATCAGGTGTCGTGGCACTTAAGAAGAGAGAATTCA

Reverse complement sequence

TGAATTCTCTCTTCTTAAGTGCCACGACACCTGATGGTATATGTGTCTTCTTGAAAGCAGCAGTAAACTCCTGCCAAGTGATAGGCTCTCCCGCAGCTCT[G/A,C]
TTTTGACGAAAGTGATCCCACCACTCAGCAGCAGGACCATGCAAATGGTGCGAAGCAAAAGAAACCTTCTCCTGCTCGGTGCACTGAATCAAATCTAACT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	87.10%	4.80%	3.17%	4.91%	G: 0.02%
All Indica	2759	90.30%	3.30%	4.06%	2.28%	NA
All Japonica	1512	83.00%	8.30%	0.60%	8.13%	NA
Aus	269	77.30%	0.00%	9.29%	13.38%	NA
Indica I	595	96.10%	0.20%	3.03%	0.67%	NA
Indica II	465	75.50%	15.70%	5.81%	3.01%	NA
Indica III	913	94.20%	0.10%	3.50%	2.19%	NA
Indica Intermediate	786	90.20%	2.20%	4.45%	3.18%	NA
Temperate Japonica	767	96.90%	0.30%	0.13%	2.74%	NA
Tropical Japonica	504	59.90%	23.60%	0.79%	15.67%	NA
Japonica Intermediate	241	87.10%	1.70%	1.66%	9.54%	NA
VI/Aromatic	96	91.70%	0.00%	3.12%	4.17%	G: 1.04%
Intermediate	90	78.90%	13.30%	1.11%	6.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1215654794	C -> DEL	LOC_Os12g26710.1	N	frameshift_variant	Average:24.47; most accessible tissue: Minghui63 flag leaf, score: 42.823	N	N	N	N
vg1215654794	C -> G	LOC_Os12g26710.1	missense_variant ; p.Asn670Lys; MODERATE	nonsynonymous_codon	Average:24.47; most accessible tissue: Minghui63 flag leaf, score: 42.823	possibly damaging	1.573	DELETERIOUS	0.01
vg1215654794	C -> T	LOC_Os12g26710.1	synonymous_variant ; p.Asn670Asn; LOW	synonymous_codon	Average:24.47; most accessible tissue: Minghui63 flag leaf, score: 42.823	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1215654794	NA	1.37E-06	mr1124	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
vg1215654794	NA	8.01E-10	mr1136	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
vg1215654794	3.82E-09	2.35E-12	mr1188	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
vg1215654794	NA	1.14E-06	mr1188	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
vg1215654794	NA	2.55E-07	mr1188	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
vg1215654794	5.95E-07	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
vg1215654794	6.43E-07	NA	mr1055_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
vg1215654794	7.71E-06	NA	mr1055_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
vg1215654794	6.98E-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
vg1215654794	NA	3.46E-08	mr1125_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
vg1215654794	1.40E-07	NA	mr1132_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
vg1215654794	1.07E-06	NA	mr1136_2	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
vg1215654794	9.01E-06	5.18E-10	mr1188_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
vg1215654794	3.57E-07	NA	mr1408_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
vg1215654794	5.69E-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
vg1215654794	6.99E-06	NA	mr1490_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
vg1215654794	2.21E-06	NA	mr1778_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
vg1215654794	4.08E-06	1.85E-06	mr1871_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