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Detailed information for vg0221843914:

Variant ID: vg0221843914 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 21843914
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AACAGCTCGTTCAGAAACGAAGTGTTGCATGTATGCACATTAATTTTTAGGCCTTGTTTAGTTCCTATTTTTTTTCCCAAAAACATCACATCGAATCTTT[G/A]
AATATATGTATGAAGCATTAAATATAGATAAAGTGAAAAACTAACTGCACAGTTTGGAAATCGCGAGACGAATCTTTTGTGCCTAATTAGTCTATGATTA

Reverse complement sequence

TAATCATAGACTAATTAGGCACAAAAGATTCGTCTCGCGATTTCCAAACTGTGCAGTTAGTTTTTCACTTTATCTATATTTAATGCTTCATACATATATT[C/T]
AAAGATTCGATGTGATGTTTTTGGGAAAAAAAATAGGAACTAAACAAGGCCTAAAAATTAATGTGCATACATGCAACACTTCGTTTCTGAACGAGCTGTT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	77.00%	18.20%	2.41%	2.39%	NA
All Indica	2759	98.90%	0.90%	0.18%	0.00%	NA
All Japonica	1512	37.30%	49.30%	6.81%	6.55%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	99.80%	0.20%	0.00%	0.00%	NA
Indica II	465	99.60%	0.20%	0.22%	0.00%	NA
Indica III	913	98.80%	1.10%	0.11%	0.00%	NA
Indica Intermediate	786	98.10%	1.50%	0.38%	0.00%	NA
Temperate Japonica	767	54.00%	36.50%	6.78%	2.74%	NA
Tropical Japonica	504	22.60%	60.90%	5.75%	10.71%	NA
Japonica Intermediate	241	14.90%	66.00%	9.13%	9.96%	NA
VI/Aromatic	96	17.70%	66.70%	3.12%	12.50%	NA
Intermediate	90	64.40%	30.00%	3.33%	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
vg0221843914	G -> A	LOC_Os02g36210.1	intron_variant ; MODIFIER	silent_mutation	Average:32.762; most accessible tissue: Callus, score: 54.091	N	N	N	N
vg0221843914	G -> DEL	N	N	silent_mutation	Average:32.762; most accessible tissue: Callus, score: 54.091	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0221843914	4.99E-06	NA	mr1534	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
vg0221843914	5.63E-06	NA	mr1042_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
vg0221843914	8.81E-06	NA	mr1305_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
vg0221843914	NA	3.01E-10	mr1379_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
vg0221843914	1.17E-06	NA	mr1543_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
vg0221843914	NA	2.07E-07	mr1554_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
vg0221843914	NA	3.54E-09	mr1559_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
vg0221843914	NA	5.30E-06	mr1559_2	Jap_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
vg0221843914	7.84E-07	NA	mr1585_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
vg0221843914	6.18E-07	NA	mr1742_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
vg0221843914	2.44E-06	NA	mr1871_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
vg0221843914	NA	1.71E-10	mr1947_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