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Detailed information for vg1220731451:

Variant ID: vg1220731451 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 20731451
Reference Allele: T	Alternative Allele: G
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GAAGGATATACCTCATCTACCCACCGTCAGCAAGTTGAGGTTAGATGTGAACACATGGTGGCATGGCCATACCATTGGTGTAACCCTTGCAAGAATCATC[T/G]
AAAGGTGTAACAACATCGAAAACATCTCCATTCGCGTCCGTGGCTTGGTAAGCTTGATCACTTAGCATATTTAATTTGTATTCATTCACTTCCTTTTAAG

Reverse complement sequence

CTTAAAAGGAAGTGAATGAATACAAATTAAATATGCTAAGTGATCAAGCTTACCAAGCCACGGACGCGAATGGAGATGTTTTCGATGTTGTTACACCTTT[A/C]
GATGATTCTTGCAAGGGTTACACCAATGGTATGGCCATGCCACCATGTGTTCACATCTAACCTCAACTTGCTGACGGTGGGTAGATGAGGTATATCCTTC

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	78.20%	21.60%	0.17%	0.00%	NA
All Indica	2759	97.80%	2.00%	0.22%	0.00%	NA
All Japonica	1512	39.00%	60.90%	0.13%	0.00%	NA
Aus	269	94.40%	5.60%	0.00%	0.00%	NA
Indica I	595	97.30%	2.20%	0.50%	0.00%	NA
Indica II	465	96.10%	3.90%	0.00%	0.00%	NA
Indica III	913	99.00%	0.90%	0.11%	0.00%	NA
Indica Intermediate	786	97.80%	1.90%	0.25%	0.00%	NA
Temperate Japonica	767	9.80%	90.20%	0.00%	0.00%	NA
Tropical Japonica	504	78.00%	21.80%	0.20%	0.00%	NA
Japonica Intermediate	241	50.20%	49.40%	0.41%	0.00%	NA
VI/Aromatic	96	96.90%	3.10%	0.00%	0.00%	NA
Intermediate	90	70.00%	30.00%	0.00%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1220731451	T -> G	LOC_Os12g34200.1	splice_region_variant&intron_variant ; LOW	silent_mutation	Average:38.499; most accessible tissue: Callus, score: 80.206	N	N	N	N
vg1220731451	T -> G	LOC_Os12g34210.1	upstream_gene_variant ; 1633.0bp to feature; MODIFIER	silent_mutation	Average:38.499; most accessible tissue: Callus, score: 80.206	N	N	N	N
vg1220731451	T -> G	LOC_Os12g34190.1	downstream_gene_variant ; 4063.0bp to feature; MODIFIER	silent_mutation	Average:38.499; most accessible tissue: Callus, score: 80.206	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1220731451	NA	2.02E-06	mr1013	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
vg1220731451	NA	2.59E-35	mr1017	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
vg1220731451	NA	1.23E-33	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
vg1220731451	NA	5.84E-15	mr1156	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
vg1220731451	NA	7.87E-06	mr1157	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
vg1220731451	NA	6.28E-06	mr1179	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
vg1220731451	NA	5.27E-06	mr1328	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
vg1220731451	6.18E-55	2.11E-162	mr1334	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
vg1220731451	6.98E-21	8.57E-35	mr1334	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
vg1220731451	NA	9.03E-06	mr1446	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
vg1220731451	NA	2.19E-06	mr1577	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
vg1220731451	NA	1.20E-10	mr1790	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
vg1220731451	NA	8.41E-08	mr1864	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
vg1220731451	NA	1.08E-46	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
vg1220731451	9.21E-69	2.98E-190	mr1334_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
vg1220731451	3.62E-21	5.97E-43	mr1334_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
vg1220731451	NA	6.62E-60	mr1390_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
vg1220731451	NA	2.11E-61	mr1490_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
vg1220731451	4.58E-23	2.30E-75	mr1991_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
vg1220731451	1.12E-14	2.68E-20	mr1991_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