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Detailed information for vg0912447596:

Variant ID: vg0912447596 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 12447596
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GAGGAGGCGAGCTCCTTGTGCTCCGACGGAGGAGGGGCTCCCACTCCGTCCCTTCGTACTCGGGTTCCGGCGACGAGAACGGTGGTGGTGGTGACGAGAA[C/T]
GCCGCGAGCTTCCATGGCAGGTTCTTGTCGCGTCCGGTGCGGGCGAGGAGGGTGCGGGGGAGGAGGTGGCGTGGCCGCCGTGTTCCGTCTCGCCGCCGGC

Reverse complement sequence

GCCGGCGGCGAGACGGAACACGGCGGCCACGCCACCTCCTCCCCCGCACCCTCCTCGCCCGCACCGGACGCGACAAGAACCTGCCATGGAAGCTCGCGGC[G/A]
TTCTCGTCACCACCACCACCGTTCTCGTCGCCGGAACCCGAGTACGAAGGGACGGAGTGGGAGCCCCTCCTCCGTCGGAGCACAAGGAGCTCGCCTCCTC

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	96.40%	0.60%	2.22%	0.72%	NA
All Indica	2759	96.60%	0.80%	2.65%	0.04%	NA
All Japonica	1512	97.60%	0.00%	0.26%	2.12%	NA
Aus	269	88.10%	1.90%	10.04%	0.00%	NA
Indica I	595	93.40%	0.70%	5.71%	0.17%	NA
Indica II	465	97.20%	0.40%	2.37%	0.00%	NA
Indica III	913	99.20%	0.30%	0.44%	0.00%	NA
Indica Intermediate	786	95.40%	1.50%	3.05%	0.00%	NA
Temperate Japonica	767	99.00%	0.00%	0.26%	0.78%	NA
Tropical Japonica	504	94.80%	0.00%	0.40%	4.76%	NA
Japonica Intermediate	241	99.20%	0.00%	0.00%	0.83%	NA
VI/Aromatic	96	95.80%	3.10%	1.04%	0.00%	NA
Intermediate	90	97.80%	1.10%	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
vg0912447596	C -> DEL	LOC_Os09g20670.1	N	frameshift_variant	Average:26.906; most accessible tissue: Zhenshan97 panicle, score: 54.901	N	N	N	N
vg0912447596	C -> T	LOC_Os09g20670.1	synonymous_variant ; p.Asn144Asn; LOW	synonymous_codon	Average:26.906; most accessible tissue: Zhenshan97 panicle, score: 54.901	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0912447596	2.06E-06	3.47E-07	mr1231	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