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Detailed information for vg0123702220:

Variant ID: vg0123702220 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 23702220
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TAATCGTGCACTCTGCACGAGTATCGACGGTCGCCTTCAAACTTAAAATCTGAGAAATATCTTGGGTAAAACTTGGGTTTTACAAAAGACTTGGAAAACC[T/C]
GACACCTGGGTCGGTGCTTGCGAACTAAATGAATTTCCAAAATCGCAGACCGGGGAACATACCGGGTGTACGGTTTCCCGCTCTTGCACTTAAGGACCGT

Reverse complement sequence

ACGGTCCTTAAGTGCAAGAGCGGGAAACCGTACACCCGGTATGTTCCCCGGTCTGCGATTTTGGAAATTCATTTAGTTCGCAAGCACCGACCCAGGTGTC[A/G]
GGTTTTCCAAGTCTTTTGTAAAACCCAAGTTTTACCCAAGATATTTCTCAGATTTTAAGTTTGAAGGCGACCGTCGATACTCGTGCAGAGTGCACGATTA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	82.90%	0.30%	6.67%	10.16%	NA
All Indica	2759	79.60%	0.40%	5.44%	14.61%	NA
All Japonica	1512	88.90%	0.00%	7.54%	3.57%	NA
Aus	269	86.20%	0.70%	11.15%	1.86%	NA
Indica I	595	65.70%	0.20%	4.87%	29.24%	NA
Indica II	465	78.30%	0.20%	7.31%	14.19%	NA
Indica III	913	90.40%	0.00%	4.93%	4.71%	NA
Indica Intermediate	786	78.20%	1.10%	5.34%	15.27%	NA
Temperate Japonica	767	99.50%	0.00%	0.39%	0.13%	NA
Tropical Japonica	504	79.80%	0.00%	12.30%	7.94%	NA
Japonica Intermediate	241	74.30%	0.00%	20.33%	5.39%	NA
VI/Aromatic	96	68.80%	0.00%	18.75%	12.50%	NA
Intermediate	90	90.00%	0.00%	3.33%	6.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0123702220	T -> DEL	LOC_Os01g41850.1	N	frameshift_variant	Average:9.658; most accessible tissue: Minghui63 panicle, score: 20.733	N	N	N	N
vg0123702220	T -> C	LOC_Os01g41850.1	missense_variant ; p.Arg66Gly; MODERATE	nonsynonymous_codon ; R66G	Average:9.658; most accessible tissue: Minghui63 panicle, score: 20.733	unknown	unknown	TOLERATED	0.53

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0123702220	1.22E-07	3.10E-10	mr1448	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
vg0123702220	3.46E-06	3.46E-06	mr1541	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