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Detailed information for vg1202795096:

Variant ID: vg1202795096 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 2795096
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CATGAAAACATAAAGGAATGGTGCGATGCAAGGTACTCACAGCACGAGCGAAGTCCTGGTTGCGGTGCCTGGCATAGAGGTCTCTAGTGCTCGCAACGTG[G/A]
GGCTGCTGCTCCAAGGGAGCGAAGGTGACCCTAGTACGGGTACGTGGCTGGTACCAGCGTAGGTAGGCCTGGTACGACTCCTCAGTGTGTGGCTCTCCCT

Reverse complement sequence

AGGGAGAGCCACACACTGAGGAGTCGTACCAGGCCTACCTACGCTGGTACCAGCCACGTACCCGTACTAGGGTCACCTTCGCTCCCTTGGAGCAGCAGCC[C/T]
CACGTTGCGAGCACTAGAGACCTCTATGCCAGGCACCGCAACCAGGACTTCGCTCGTGCTGTGAGTACCTTGCATCGCACCATTCCTTTATGTTTTCATG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	95.10%	2.00%	1.23%	1.69%	NA
All Indica	2759	95.30%	3.10%	1.34%	0.29%	NA
All Japonica	1512	99.00%	0.70%	0.13%	0.20%	NA
Aus	269	68.00%	0.00%	6.69%	25.28%	NA
Indica I	595	87.60%	8.10%	4.37%	0.00%	NA
Indica II	465	99.60%	0.40%	0.00%	0.00%	NA
Indica III	913	98.50%	0.90%	0.44%	0.22%	NA
Indica Intermediate	786	94.90%	3.40%	0.89%	0.76%	NA
Temperate Japonica	767	99.70%	0.00%	0.26%	0.00%	NA
Tropical Japonica	504	98.20%	1.20%	0.00%	0.60%	NA
Japonica Intermediate	241	98.30%	1.70%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	97.80%	0.00%	1.11%	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
vg1202795096	G -> DEL	LOC_Os12g06040.1	N	frameshift_variant	Average:54.406; most accessible tissue: Minghui63 flag leaf, score: 75.341	N	N	N	N
vg1202795096	G -> A	LOC_Os12g06040.1	synonymous_variant ; p.Pro1321Pro; LOW	synonymous_codon	Average:54.406; most accessible tissue: Minghui63 flag leaf, score: 75.341	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1202795096	NA	2.80E-08	mr1070	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
vg1202795096	NA	2.81E-08	mr1128	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
vg1202795096	NA	1.62E-06	mr1692	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
vg1202795096	NA	4.58E-08	mr1740	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
vg1202795096	NA	1.72E-07	mr1128_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