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Detailed information for vg1213044906:

Variant ID: vg1213044906 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 13044906
Reference Allele: C	Alternative Allele: G
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AAATTTTAGTACCAGTGTTTGTATTAAAACAACGATGGTTCTGTCCACCATCCATTGTGATCCCAAGGATAGCTTCCCGCCATTGAGTCGTTATGGTTTT[C/G]
TGAGGACGCCTACCTTCCCCCTTCTCAGGAAGTGGCTCCAACAGCATAAAAATTCGTCATGCAACAACCCATCCCACACAAGTTAAGAATTTAGAGACTA

Reverse complement sequence

TAGTCTCTAAATTCTTAACTTGTGTGGGATGGGTTGTTGCATGACGAATTTTTATGCTGTTGGAGCCACTTCCTGAGAAGGGGGAAGGTAGGCGTCCTCA[G/C]
AAAACCATAACGACTCAATGGCGGGAAGCTATCCTTGGGATCACAATGGATGGTGGACAGAACCATCGTTGTTTTAATACAAACACTGGTACTAAAATTT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	54.30%	1.60%	16.10%	28.08%	NA
All Indica	2759	62.30%	0.00%	17.07%	20.66%	NA
All Japonica	1512	44.40%	4.80%	4.43%	46.36%	NA
Aus	269	33.50%	0.00%	57.99%	8.55%	NA
Indica I	595	40.80%	0.00%	17.82%	41.34%	NA
Indica II	465	49.20%	0.00%	21.29%	29.46%	NA
Indica III	913	82.10%	0.00%	14.35%	3.50%	NA
Indica Intermediate	786	63.10%	0.00%	17.18%	19.72%	NA
Temperate Japonica	767	78.20%	0.10%	1.17%	20.47%	NA
Tropical Japonica	504	2.60%	7.50%	6.55%	83.33%	NA
Japonica Intermediate	241	24.50%	13.70%	10.37%	51.45%	NA
VI/Aromatic	96	41.70%	0.00%	44.79%	13.54%	NA
Intermediate	90	48.90%	2.20%	26.67%	22.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1213044906	C -> DEL	N	N	silent_mutation	Average:8.263; most accessible tissue: Minghui63 root, score: 13.235	N	N	N	N
vg1213044906	C -> G	LOC_Os12g23070.1	upstream_gene_variant ; 4428.0bp to feature; MODIFIER	silent_mutation	Average:8.263; most accessible tissue: Minghui63 root, score: 13.235	N	N	N	N
vg1213044906	C -> G	LOC_Os12g23080.1	upstream_gene_variant ; 1969.0bp to feature; MODIFIER	silent_mutation	Average:8.263; most accessible tissue: Minghui63 root, score: 13.235	N	N	N	N
vg1213044906	C -> G	LOC_Os12g23080-LOC_Os12g23090	intergenic_region ; MODIFIER	silent_mutation	Average:8.263; most accessible tissue: Minghui63 root, score: 13.235	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1213044906	1.85E-06	1.85E-06	mr1877_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