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Detailed information for vg1122916451:

Variant ID: vg1122916451 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 22916451
Reference Allele: T	Alternative Allele: G,A
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GCGACCAGGACAAGTGGCTCAGCTCTGATGCCAAAACTGTTGAGGTAGATAACTTGCTCTCCTGGCCTCTGCAGCAGCAAAGTGAGACCCTGTTTAGATG[T/G,A]
GACTAAAACTAAGTCCCTATCACATCGGATATTTGGACACTAATTATAAATATTAAACATAGACTATTAATAAAACCCATCAATAATCTTGGACTAATTC

Reverse complement sequence

GAATTAGTCCAAGATTATTGATGGGTTTTATTAATAGTCTATGTTTAATATTTATAATTAGTGTCCAAATATCCGATGTGATAGGGACTTAGTTTTAGTC[A/C,T]
CATCTAAACAGGGTCTCACTTTGCTGCTGCAGAGGCCAGGAGAGCAAGTTATCTACCTCAACAGTTTTGGCATCAGAGCTGAGCCACTTGTCCTGGTCGC

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	94.30%	5.10%	0.13%	0.00%	A: 0.55%
All Indica	2759	99.20%	0.60%	0.00%	0.00%	A: 0.18%
All Japonica	1512	85.30%	14.30%	0.33%	0.00%	A: 0.07%
Aus	269	93.70%	0.00%	0.00%	0.00%	A: 6.32%
Indica I	595	99.20%	0.80%	0.00%	0.00%	NA
Indica II	465	98.90%	1.10%	0.00%	0.00%	NA
Indica III	913	99.70%	0.20%	0.00%	0.00%	A: 0.11%
Indica Intermediate	786	98.90%	0.60%	0.00%	0.00%	A: 0.51%
Temperate Japonica	767	73.40%	26.10%	0.52%	0.00%	NA
Tropical Japonica	504	99.60%	0.20%	0.20%	0.00%	NA
Japonica Intermediate	241	93.40%	6.20%	0.00%	0.00%	A: 0.41%
VI/Aromatic	96	95.80%	0.00%	1.04%	0.00%	A: 3.12%
Intermediate	90	93.30%	6.70%	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
vg1122916451	T -> A	LOC_Os11g38640.1	intron_variant ; MODIFIER	silent_mutation	Average:71.846; most accessible tissue: Minghui63 panicle, score: 86.442	N	N	N	N
vg1122916451	T -> G	LOC_Os11g38640.1	intron_variant ; MODIFIER	silent_mutation	Average:71.846; most accessible tissue: Minghui63 panicle, score: 86.442	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1122916451	1.24E-06	1.24E-06	mr1273_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
vg1122916451	4.58E-06	4.58E-06	mr1355_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