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Detailed information for vg0427970215:

Variant ID: vg0427970215 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 27970215
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACCGAGTTAAATATGAGGCAAAGAAGATGGCTGGAACTAATCAAGGATTACGATCTTGGAATCCATTACCATCCTGGTAAAGCTAACGTGGTCGCTGATG[C/T]
GCTAAGTCGCAAGGTCTATTGCAACGTAGCTCAAATATGGCCTGACCAAGATCGCCTGTGCAGAGAATTGGAGAAGTTGAGGCTGACCGTGGTACAGTCA

Reverse complement sequence

TGACTGTACCACGGTCAGCCTCAACTTCTCCAATTCTCTGCACAGGCGATCTTGGTCAGGCCATATTTGAGCTACGTTGCAATAGACCTTGCGACTTAGC[G/A]
CATCAGCGACCACGTTAGCTTTACCAGGATGGTAATGGATTCCAAGATCGTAATCCTTGATTAGTTCCAGCCATCTTCTTTGCCTCATATTTAACTCGGT

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	52.00%	0.30%	6.92%	40.84%	NA
All Indica	2759	23.50%	0.40%	10.69%	65.42%	NA
All Japonica	1512	99.70%	0.00%	0.00%	0.33%	NA
Aus	269	52.40%	0.40%	10.78%	36.43%	NA
Indica I	595	22.00%	0.50%	7.39%	70.08%	NA
Indica II	465	14.00%	1.10%	6.67%	78.28%	NA
Indica III	913	28.30%	0.10%	15.77%	55.86%	NA
Indica Intermediate	786	24.60%	0.40%	9.67%	65.39%	NA
Temperate Japonica	767	99.70%	0.00%	0.00%	0.26%	NA
Tropical Japonica	504	99.80%	0.00%	0.00%	0.20%	NA
Japonica Intermediate	241	99.20%	0.00%	0.00%	0.83%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	72.20%	0.00%	3.33%	24.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0427970215	C -> DEL	LOC_Os04g47100.1	N	frameshift_variant	Average:6.792; most accessible tissue: Minghui63 young leaf, score: 11.521	N	N	N	N
vg0427970215	C -> T	LOC_Os04g47100.1	missense_variant ; p.Ala1332Val; MODERATE	nonsynonymous_codon ; A1332V	Average:6.792; most accessible tissue: Minghui63 young leaf, score: 11.521	benign	1.39	DELETERIOUS	0.00

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0427970215	NA	3.85E-08	mr1050_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
vg0427970215	NA	3.99E-06	mr1245_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
vg0427970215	NA	6.39E-07	mr1278_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
vg0427970215	NA	8.82E-07	mr1329_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
vg0427970215	NA	7.08E-06	mr1337_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
vg0427970215	NA	6.83E-06	mr1445_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
vg0427970215	NA	1.77E-08	mr1449_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
vg0427970215	NA	5.06E-09	mr1690_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