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Detailed information for vg0912513638:

Variant ID: vg0912513638 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 12513638
Reference Allele: A	Alternative Allele: C
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTGCACCGGCAAAATACGGGGAACGCCCCCTGCTCCTCGAGTTACCGCCTTCCGCCGCTGCCCGCTGATAACATCTCGCCGCGCGGCCGTGGCCGGGGAA[A/C]
TGTCGAATTAGCTAGGAAGAAAAAAAGGGAATTGCTATCCTTCTTTCGATAGAAATTGCATCCTCAAATCTTGCAGATTTTAGGATACTGGATGAGCTTC

Reverse complement sequence

GAAGCTCATCCAGTATCCTAAAATCTGCAAGATTTGAGGATGCAATTTCTATCGAAAGAAGGATAGCAATTCCCTTTTTTTCTTCCTAGCTAATTCGACA[T/G]
TTCCCCGGCCACGGCCGCGCGGCGAGATGTTATCAGCGGGCAGCGGCGGAAGGCGGTAACTCGAGGAGCAGGGGGCGTTCCCCGTATTTTGCCGGTGCAA

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	58.00%	0.80%	1.74%	39.55%	NA
All Indica	2759	35.20%	1.20%	1.30%	62.31%	NA
All Japonica	1512	94.80%	0.20%	0.20%	4.83%	NA
Aus	269	64.70%	0.00%	15.24%	20.07%	NA
Indica I	595	21.50%	1.50%	1.68%	75.29%	NA
Indica II	465	21.50%	0.60%	1.29%	76.56%	NA
Indica III	913	51.90%	1.10%	0.99%	46.00%	NA
Indica Intermediate	786	34.40%	1.30%	1.40%	62.98%	NA
Temperate Japonica	767	98.20%	0.10%	0.00%	1.69%	NA
Tropical Japonica	504	89.10%	0.40%	0.40%	10.12%	NA
Japonica Intermediate	241	95.90%	0.00%	0.41%	3.73%	NA
VI/Aromatic	96	92.70%	1.00%	2.08%	4.17%	NA
Intermediate	90	78.90%	0.00%	0.00%	21.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0912513638	A -> DEL	N	N	silent_mutation	Average:19.724; most accessible tissue: Minghui63 root, score: 56.226	N	N	N	N
vg0912513638	A -> C	LOC_Os09g20760.1	upstream_gene_variant ; 4195.0bp to feature; MODIFIER	silent_mutation	Average:19.724; most accessible tissue: Minghui63 root, score: 56.226	N	N	N	N
vg0912513638	A -> C	LOC_Os09g20770.1	intron_variant ; MODIFIER	silent_mutation	Average:19.724; most accessible tissue: Minghui63 root, score: 56.226	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0912513638	9.18E-07	6.63E-07	mr1172_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