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Detailed information for vg0406063032:

Variant ID: vg0406063032 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 6063032
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTGTTGTTTTTGCTGGTTGTGTTGCTAGTCATGATGAATGGATACTTGATACTGCATGTTCTTTTCATATCTGCATTAACAGAGATTGGTTTAGTTCTTA[C/T]
AAGTCTGTGCAGAATGGAGATGTTGTGTGCATGGGAGATGATAACCCACGTGAGATTGTAGGCATTGGCTCCGTTTAGATCAAGACTCATGATGGCATGA

Reverse complement sequence

TCATGCCATCATGAGTCTTGATCTAAACGGAGCCAATGCCTACAATCTCACGTGGGTTATCATCTCCCATGCACACAACATCTCCATTCTGCACAGACTT[G/A]
TAAGAACTAAACCAATCTCTGTTAATGCAGATATGAAAAGAACATGCAGTATCAAGTATCCATTCATCATGACTAGCAACACAACCAGCAAAAACAACAA

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	96.60%	2.00%	0.80%	0.57%	NA
All Indica	2759	95.50%	3.30%	1.20%	0.00%	NA
All Japonica	1512	98.10%	0.10%	0.00%	1.79%	NA
Aus	269	98.10%	0.70%	1.12%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	81.70%	15.70%	2.58%	0.00%	NA
Indica III	913	97.50%	0.90%	1.64%	0.00%	NA
Indica Intermediate	786	97.80%	1.40%	0.76%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	95.60%	0.00%	0.00%	4.37%	NA
Japonica Intermediate	241	97.50%	0.40%	0.00%	2.07%	NA
VI/Aromatic	96	97.90%	0.00%	2.08%	0.00%	NA
Intermediate	90	98.90%	1.10%	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
vg0406063032	C -> DEL	LOC_Os04g11150.1	N	frameshift_variant	Average:14.389; most accessible tissue: Callus, score: 34.191	N	N	N	N
vg0406063032	C -> T	LOC_Os04g11150.1	missense_variant ; p.Thr181Ile; MODERATE	nonsynonymous_codon ; T181I	Average:14.389; most accessible tissue: Callus, score: 34.191	unknown	unknown	TOLERATED	0.39

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0406063032	3.96E-06	NA	mr1216	Ind_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