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Detailed information for vg1127797000:

Variant ID: vg1127797000 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 27797000
Reference Allele: C	Alternative Allele: G
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 263. )

Flanking Sequence (100 bp) in Reference Genome:

CCTGCGACGCCTGTGCTTTGTCATGAAAATTATGACTTCAGCTCTAACAACAATTGAACAAGGGGCTCTATCGAACCTCGTCTCGCTTCAGCTGCTCTGT[C/G]
AAGGTCTAGTTGGTCTTTCCGGCATTGAGATCAGACACCTGAAACATCTTAAGGAAATCACCATCGACTCTGCAGTGACTGTACAAACAAGACAAGATTG

Reverse complement sequence

CAATCTTGTCTTGTTTGTACAGTCACTGCAGAGTCGATGGTGATTTCCTTAAGATGTTTCAGGTGTCTGATCTCAATGCCGGAAAGACCAACTAGACCTT[G/C]
ACAGAGCAGCTGAAGCGAGACGAGGTTCGATAGAGCCCCTTGTTCAATTGTTGTTAGAGCTGAAGTCATAATTTTCATGACAAAGCACAGGCGTCGCAGG

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	96.00%	0.30%	0.19%	3.51%	NA
All Indica	2759	93.40%	0.50%	0.33%	5.76%	NA
All Japonica	1512	99.70%	0.10%	0.00%	0.20%	NA
Aus	269	98.90%	0.40%	0.00%	0.74%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	80.60%	1.90%	0.86%	16.56%	NA
Indica III	913	98.20%	0.00%	0.00%	1.75%	NA
Indica Intermediate	786	90.30%	0.60%	0.64%	8.40%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.20%	0.20%	0.00%	0.60%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	97.80%	0.00%	0.00%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1127797000	C -> DEL	LOC_Os11g45930.1	N	frameshift_variant	Average:70.409; most accessible tissue: Zhenshan97 flower, score: 86.268	N	N	N	N
vg1127797000	C -> G	LOC_Os11g45930.1	missense_variant ; p.Gln973Glu; MODERATE	nonsynonymous_codon ; Q973E	Average:70.409; most accessible tissue: Zhenshan97 flower, score: 86.268	benign	0.998	TOLERATED	0.36

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1127797000	2.09E-08	3.02E-09	mr1238	Ind_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
vg1127797000	NA	5.38E-06	mr1309	Ind_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
vg1127797000	NA	1.38E-06	mr1841	Ind_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
vg1127797000	7.87E-11	4.64E-11	mr1238_2	Ind_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
vg1127797000	4.92E-12	1.95E-12	mr1484_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
vg1127797000	1.62E-11	4.35E-11	mr1841_2	Ind_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
vg1127797000	1.42E-07	3.33E-08	mr1900_2	Ind_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
vg1127797000	1.44E-09	1.44E-09	mr1945_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