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Detailed information for vg1206964772:

Variant ID: vg1206964772 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 6964772
Reference Allele: C	Alternative Allele: A
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATTCCACTGACCGCTTCTTCATCGTCAATCTCCAGCCACCGCTGGCCTTCGTGAGCCATTTTGCCGCTTCGCCCACAGTTGTCCAGCAGGAACTCAACCG[C/A]
TGGGCGCTACCAGTCGTCGCACAACCATCTCGGTCGGAAGTGCTGGGTTGCTTCTAACTAAAATTACTAAAGAAAATCTGGTCATGAATTGCACAACTTG

Reverse complement sequence

CAAGTTGTGCAATTCATGACCAGATTTTCTTTAGTAATTTTAGTTAGAAGCAACCCAGCACTTCCGACCGAGATGGTTGTGCGACGACTGGTAGCGCCCA[G/T]
CGGTTGAGTTCCTGCTGGACAACTGTGGGCGAAGCGGCAAAATGGCTCACGAAGGCCAGCGGTGGCTGGAGATTGACGATGAAGAAGCGGTCAGTGGAAT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	59.10%	14.70%	0.99%	25.24%	NA
All Indica	2759	89.30%	7.50%	0.14%	3.08%	NA
All Japonica	1512	5.40%	28.30%	1.06%	65.28%	NA
Aus	269	57.60%	14.90%	1.12%	26.39%	NA
Indica I	595	92.40%	6.20%	0.00%	1.34%	NA
Indica II	465	95.70%	1.50%	0.22%	2.58%	NA
Indica III	913	86.20%	10.60%	0.00%	3.18%	NA
Indica Intermediate	786	86.60%	8.40%	0.38%	4.58%	NA
Temperate Japonica	767	7.40%	31.70%	1.43%	59.45%	NA
Tropical Japonica	504	4.00%	16.30%	0.79%	78.97%	NA
Japonica Intermediate	241	1.70%	42.70%	0.41%	55.19%	NA
VI/Aromatic	96	54.20%	7.30%	17.71%	20.83%	NA
Intermediate	90	44.40%	14.40%	7.78%	33.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1206964772	C -> DEL	N	N	silent_mutation	Average:49.603; most accessible tissue: Minghui63 root, score: 63.193	N	N	N	N
vg1206964772	C -> A	LOC_Os12g12640.1	downstream_gene_variant ; 844.0bp to feature; MODIFIER	silent_mutation	Average:49.603; most accessible tissue: Minghui63 root, score: 63.193	N	N	N	N
vg1206964772	C -> A	LOC_Os12g12630-LOC_Os12g12640	intergenic_region ; MODIFIER	silent_mutation	Average:49.603; most accessible tissue: Minghui63 root, score: 63.193	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1206964772	1.58E-07	2.79E-08	mr1565_2	Jap_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