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Detailed information for vg1012841072:

Variant ID: vg1012841072 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 12841072
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 304. )

Flanking Sequence (100 bp) in Reference Genome:

TGATAGATATCTGAGGCATGCTACAATCAATGGGAAAGGAAATCACATCGTTTCCGCTCCCTGAAATTGACGAATCACATGATAGTACCAGAGGAGATCC[C/T]
AGAGAGATTATTGAGGAGTCATCCATTGGTGTGGAGACGGACGATATGAACCTCTCAGACCAGCTGAATGATGAGCAAAGGTCCGCATTCAACAAAATCA

Reverse complement sequence

TGATTTTGTTGAATGCGGACCTTTGCTCATCATTCAGCTGGTCTGAGAGGTTCATATCGTCCGTCTCCACACCAATGGATGACTCCTCAATAATCTCTCT[G/A]
GGATCTCCTCTGGTACTATCATGTGATTCGTCAATTTCAGGGAGCGGAAACGATGTGATTTCCTTTCCCATTGATTGTAGCATGCCTCAGATATCTATCA

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	56.50%	19.70%	14.96%	8.91%	NA
All Indica	2759	30.60%	32.70%	23.67%	13.05%	NA
All Japonica	1512	96.60%	0.10%	1.06%	2.18%	NA
Aus	269	89.60%	4.50%	5.58%	0.37%	NA
Indica I	595	44.70%	24.50%	22.86%	7.90%	NA
Indica II	465	24.50%	32.30%	22.80%	20.43%	NA
Indica III	913	23.20%	39.00%	24.10%	13.69%	NA
Indica Intermediate	786	31.90%	31.90%	24.30%	11.83%	NA
Temperate Japonica	767	97.90%	0.10%	1.04%	0.91%	NA
Tropical Japonica	504	98.00%	0.00%	0.60%	1.39%	NA
Japonica Intermediate	241	89.60%	0.40%	2.07%	7.88%	NA
VI/Aromatic	96	66.70%	2.10%	12.50%	18.75%	NA
Intermediate	90	66.70%	11.10%	12.22%	10.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1012841072	C -> T	LOC_Os10g24940.1	synonymous_variant ; p.Pro1309Pro; LOW	synonymous_codon	Average:11.13; most accessible tissue: Callus, score: 44.136	N	N	N	N
vg1012841072	C -> DEL	LOC_Os10g24940.1	N	frameshift_variant	Average:11.13; most accessible tissue: Callus, score: 44.136	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1012841072	4.37E-06	NA	mr1868	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
vg1012841072	3.02E-06	NA	mr1868	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