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Detailed information for vg1127402538:

Variant ID: vg1127402538 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 27402538
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: 263. )

Flanking Sequence (100 bp) in Reference Genome:

GGAGGATAGCTCAGGTGCGAAGCCACCGGGTGACTAAAGTAATAACCTCTAGATCGTGAATTCCAAGCCCACCTTAATCTTTGGGACGACAAATAATGTC[C/T]
CACTTAGCAAGCCGATATTTTTTCTTATGTCCATCCCCTTGCCAATAGAACCTAGATCGAAAGTAGTCAAGTTTCTTACATACCCCGCTAGGTATTGCAA

Reverse complement sequence

TTGCAATACCTAGCGGGGTATGTAAGAAACTTGACTACTTTCGATCTAGGTTCTATTGGCAAGGGGATGGACATAAGAAAAAATATCGGCTTGCTAAGTG[G/A]
GACATTATTTGTCGTCCCAAAGATTAAGGTGGGCTTGGAATTCACGATCTAGAGGTTATTACTTTAGTCACCCGGTGGCTTCGCACCTGAGCTATCCTCC

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	99.00%	0.80%	0.15%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.00%	0.00%	NA
All Japonica	1512	97.00%	2.50%	0.46%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	100.00%	0.00%	0.00%	0.00%	NA
Temperate Japonica	767	96.20%	3.00%	0.78%	0.00%	NA
Tropical Japonica	504	99.60%	0.40%	0.00%	0.00%	NA
Japonica Intermediate	241	94.20%	5.40%	0.41%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	100.00%	0.00%	0.00%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1127402538	C -> T	LOC_Os11g45280.1	intron_variant ; MODIFIER	silent_mutation	Average:66.736; most accessible tissue: Minghui63 flag leaf, score: 83.197	N	N	N	N
vg1127402538	C -> T	LOC_Os11g45280.2	intron_variant ; MODIFIER	silent_mutation	Average:66.736; most accessible tissue: Minghui63 flag leaf, score: 83.197	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1127402538	2.09E-17	2.09E-17	mr1191_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