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Detailed information for vg1122387797:

Variant ID: vg1122387797 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 22387797
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.76, A: 0.24, others allele: 0.00, population size: 70. )

Flanking Sequence (100 bp) in Reference Genome:

TCATTCGTGCTGGTAGCCAGGTACATGCACCAAATTAAGTAGCACAGCAACATCTTCACAACATTCTTCAACTTAGGTCATAGCTAAAAATTAAGGAGCA[C/A]
ATGACAGGGGCATGACAACTCTTTTCCTGCTGTAACTAAGGAGCACAGGACAGGAGCAGCTCGATGCCATCTGGACTCCACCTCTTTATCTCAAGGATTT

Reverse complement sequence

AAATCCTTGAGATAAAGAGGTGGAGTCCAGATGGCATCGAGCTGCTCCTGTCCTGTGCTCCTTAGTTACAGCAGGAAAAGAGTTGTCATGCCCCTGTCAT[G/T]
TGCTCCTTAATTTTTAGCTATGACCTAAGTTGAAGAATGTTGTGAAGATGTTGCTGTGCTACTTAATTTGGTGCATGTACCTGGCTACCAGCACGAATGA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	29.80%	10.80%	0.34%	59.10%	NA
All Indica	2759	17.40%	14.30%	0.11%	68.18%	NA
All Japonica	1512	56.40%	1.30%	0.79%	41.47%	NA
Aus	269	15.60%	0.40%	0.37%	83.64%	NA
Indica I	595	36.80%	11.60%	0.17%	51.43%	NA
Indica II	465	22.40%	1.50%	0.00%	76.13%	NA
Indica III	913	0.80%	27.30%	0.11%	71.85%	NA
Indica Intermediate	786	19.20%	8.80%	0.13%	71.88%	NA
Temperate Japonica	767	82.00%	1.70%	0.26%	16.04%	NA
Tropical Japonica	504	21.60%	0.40%	1.39%	76.59%	NA
Japonica Intermediate	241	47.70%	2.10%	1.24%	48.96%	NA
VI/Aromatic	96	2.10%	81.20%	0.00%	16.67%	NA
Intermediate	90	33.30%	17.80%	0.00%	48.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1122387797	C -> A	LOC_Os11g37790.1	downstream_gene_variant ; 3036.0bp to feature; MODIFIER	silent_mutation	Average:17.193; most accessible tissue: Callus, score: 94.488	N	N	N	N
vg1122387797	C -> A	LOC_Os11g37800.1	intron_variant ; MODIFIER	silent_mutation	Average:17.193; most accessible tissue: Callus, score: 94.488	N	N	N	N
vg1122387797	C -> DEL	N	N	silent_mutation	Average:17.193; most accessible tissue: Callus, score: 94.488	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1122387797	NA	5.95E-08	mr1438_2	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
vg1122387797	NA	6.01E-06	mr1908_2	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
vg1122387797	NA	3.71E-10	mr1994_2	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