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Detailed information for vg0403292001:

Variant ID: vg0403292001 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 3292001
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCGGGTTTTTGTTCAAGGAGCACGGTTAGACCGCAGCTAAACCGGCTGCCAGGCCCGGTTAGACCGCAGGGACAGCGGCGGTCAGACCGGCCCCGGGGCA[A/G]
TTTTGCACGTAATTCAAATCGGACTTTTGTGAAGCGACAAGGTAAGTTTTCAGGTAAGTCTGGTTCTGATTTTGTTAGTGCATATAGTGCATATGTACCT

Reverse complement sequence

AGGTACATATGCACTATATGCACTAACAAAATCAGAACCAGACTTACCTGAAAACTTACCTTGTCGCTTCACAAAAGTCCGATTTGAATTACGTGCAAAA[T/C]
TGCCCCGGGGCCGGTCTGACCGCCGCTGTCCCTGCGGTCTAACCGGGCCTGGCAGCCGGTTTAGCTGCGGTCTAACCGTGCTCCTTGAACAAAAACCCGA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	89.00%	0.20%	0.49%	10.26%	NA
All Indica	2759	99.50%	0.40%	0.07%	0.04%	NA
All Japonica	1512	69.80%	0.00%	0.93%	29.30%	NA
Aus	269	96.70%	0.00%	1.86%	1.49%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.80%	0.00%	0.00%	0.22%	NA
Indica III	913	98.80%	1.20%	0.00%	0.00%	NA
Indica Intermediate	786	99.70%	0.00%	0.25%	0.00%	NA
Temperate Japonica	767	88.90%	0.00%	0.13%	10.95%	NA
Tropical Japonica	504	47.20%	0.00%	1.98%	50.79%	NA
Japonica Intermediate	241	56.00%	0.00%	1.24%	42.74%	NA
VI/Aromatic	96	62.50%	0.00%	2.08%	35.42%	NA
Intermediate	90	96.70%	0.00%	0.00%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0403292001	A -> DEL	LOC_Os04g06290.1	N	frameshift_variant	Average:19.405; most accessible tissue: Callus, score: 26.096	N	N	N	N
vg0403292001	A -> G	LOC_Os04g06290.1	missense_variant ; p.Asn612Ser; MODERATE	nonsynonymous_codon	Average:19.405; most accessible tissue: Callus, score: 26.096	unknown	unknown	TOLERATED	0.78

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0403292001	3.62E-06	5.95E-08	mr1728	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