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Detailed information for vg0622963600:

Variant ID: vg0622963600 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 22963600
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGCCAGTAGGTAGCTGCTCTAGCAGTTAGCAATGCTTGCAGCTTGACGACGACTCAACAATCTTCTGGTAATGGAGGACGGTTCTCCCAGCACGTCCCTG[T/C]
AGTCTCTCAGGGATGATTCTTCAGATACTCAGGAAGCCGGTGTGTAGGGAAGTAACGATCCTCGTCGCTCGGATCCATTGGTGGATCTGCAGCACATCAC

Reverse complement sequence

GTGATGTGCTGCAGATCCACCAATGGATCCGAGCGACGAGGATCGTTACTTCCCTACACACCGGCTTCCTGAGTATCTGAAGAATCATCCCTGAGAGACT[A/G]
CAGGGACGTGCTGGGAGAACCGTCCTCCATTACCAGAAGATTGTTGAGTCGTCGTCAAGCTGCAAGCATTGCTAACTGCTAGAGCAGCTACCTACTGGCT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	89.90%	6.00%	0.04%	4.08%	NA
All Indica	2759	98.00%	0.70%	0.04%	1.30%	NA
All Japonica	1512	82.50%	16.50%	0.00%	0.93%	NA
Aus	269	43.90%	3.70%	0.37%	52.04%	NA
Indica I	595	99.80%	0.20%	0.00%	0.00%	NA
Indica II	465	98.10%	0.00%	0.00%	1.94%	NA
Indica III	913	97.30%	1.30%	0.11%	1.31%	NA
Indica Intermediate	786	97.50%	0.60%	0.00%	1.91%	NA
Temperate Japonica	767	72.40%	27.50%	0.00%	0.13%	NA
Tropical Japonica	504	93.10%	4.60%	0.00%	2.38%	NA
Japonica Intermediate	241	92.90%	6.60%	0.00%	0.41%	NA
VI/Aromatic	96	96.90%	1.00%	0.00%	2.08%	NA
Intermediate	90	94.40%	4.40%	0.00%	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
vg0622963600	T -> C	LOC_Os06g38670.1	synonymous_variant ; p.Cys1212Cys; LOW	synonymous_codon	Average:47.832; most accessible tissue: Zhenshan97 panicle, score: 83.41	N	N	N	N
vg0622963600	T -> DEL	LOC_Os06g38670.1	N	frameshift_variant	Average:47.832; most accessible tissue: Zhenshan97 panicle, score: 83.41	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0622963600	NA	9.34E-06	mr1305	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
vg0622963600	5.19E-06	NA	mr1585	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
vg0622963600	NA	1.53E-07	mr1585	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
vg0622963600	NA	9.41E-06	mr1765	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
vg0622963600	NA	2.15E-09	mr1915	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
vg0622963600	NA	2.99E-06	mr1439_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
vg0622963600	2.96E-06	2.96E-06	mr1571_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
vg0622963600	NA	3.32E-06	mr1915_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