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Detailed information for vg0400033101:

Variant ID: vg0400033101 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 33101
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 90. )

Flanking Sequence (100 bp) in Reference Genome:

TTCACCAGCGCTACCCGGACGAGTTGCAGCACTCGCCCTACCGTTACCACCCTCGTCGCGGAGGAGCCCGCGACTACGCCACCTTCTGGGATGCTAGCTC[A/G]
GAGGATGACGCTACCATCATGCACCTGGCGCGCATGGTGGAGGCGTACGACGCGGCCCGTATCGACTTCCATCAGATGGTGCGTCGCGGGTTGGTCGAGA

Reverse complement sequence

TCTCGACCAACCCGCGACGCACCATCTGATGGAAGTCGATACGGGCCGCGTCGTACGCCTCCACCATGCGCGCCAGGTGCATGATGGTAGCGTCATCCTC[T/C]
GAGCTAGCATCCCAGAAGGTGGCGTAGTCGCGGGCTCCTCCGCGACGAGGGTGGTAACGGTAGGGCGAGTGCTGCAACTCGTCCGGGTAGCGCTGGTGAA

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	26.50%	10.50%	37.03%	25.98%	NA
All Indica	2759	14.60%	1.00%	40.78%	43.57%	NA
All Japonica	1512	31.50%	30.10%	37.76%	0.66%	NA
Aus	269	98.50%	0.40%	1.12%	0.00%	NA
Indica I	595	4.70%	0.30%	30.92%	64.03%	NA
Indica II	465	11.40%	0.40%	28.39%	59.78%	NA
Indica III	913	20.70%	1.60%	50.16%	27.49%	NA
Indica Intermediate	786	17.00%	1.10%	44.66%	37.15%	NA
Temperate Japonica	767	51.10%	32.30%	16.43%	0.13%	NA
Tropical Japonica	504	8.90%	23.80%	66.67%	0.60%	NA
Japonica Intermediate	241	16.20%	36.10%	45.23%	2.49%	NA
VI/Aromatic	96	83.30%	5.20%	9.38%	2.08%	NA
Intermediate	90	31.10%	6.70%	46.67%	15.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0400033101	A -> DEL	LOC_Os04g01040.1	N	frameshift_variant	Average:22.406; most accessible tissue: Zhenshan97 flag leaf, score: 31.305	N	N	N	N
vg0400033101	A -> G	LOC_Os04g01040.1	synonymous_variant ; p.Ser193Ser; LOW	synonymous_codon	Average:22.406; most accessible tissue: Zhenshan97 flag leaf, score: 31.305	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0400033101	9.87E-06	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
vg0400033101	5.77E-08	NA	mr1670_2	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
vg0400033101	6.36E-07	6.36E-07	mr1670_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
vg0400033101	NA	1.63E-06	mr1780_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