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Detailed information for vg0804028565:

Variant ID: vg0804028565 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 4028565
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CGTGGCACACCCCATGAGTAATGGACAAGTTGAGCGCGCCAATGGCATGGTACTTAAAGGGATAAAAGCACAAGTTTTCGACCGACTACGTCCCTATGTT[G/A]
GCAAGTGGGTAGATCAGCTGCCGTCCATACTTTGGTCGTTACGCACTACTCCCAGTCGGGCTACCGGCCAGTCGCCGTTCTTTTTGGTCTATGGTGCAGA

Reverse complement sequence

TCTGCACCATAGACCAAAAAGAACGGCGACTGGCCGGTAGCCCGACTGGGAGTAGTGCGTAACGACCAAAGTATGGACGGCAGCTGATCTACCCACTTGC[C/T]
AACATAGGGACGTAGTCGGTCGAAAACTTGTGCTTTTATCCCTTTAAGTACCATGCCATTGGCGCGCTCAACTTGTCCATTACTCATGGGGTGTGCCACG

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	41.00%	4.30%	14.39%	40.37%	NA
All Indica	2759	24.40%	0.20%	16.24%	59.19%	NA
All Japonica	1512	79.60%	12.60%	3.90%	3.97%	NA
Aus	269	3.00%	0.00%	47.21%	49.81%	NA
Indica I	595	12.90%	0.20%	10.92%	75.97%	NA
Indica II	465	74.40%	0.40%	6.88%	18.28%	NA
Indica III	913	7.40%	0.00%	22.89%	69.66%	NA
Indica Intermediate	786	23.20%	0.30%	18.07%	58.52%	NA
Temperate Japonica	767	95.80%	0.00%	2.09%	2.09%	NA
Tropical Japonica	504	48.40%	36.90%	6.15%	8.53%	NA
Japonica Intermediate	241	92.90%	1.70%	4.98%	0.41%	NA
VI/Aromatic	96	11.50%	0.00%	28.12%	60.42%	NA
Intermediate	90	45.60%	7.80%	21.11%	25.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0804028565	G -> A	LOC_Os08g07220.1	missense_variant ; p.Gly936Ser; MODERATE	nonsynonymous_codon ; G936S	Average:27.455; most accessible tissue: Minghui63 flag leaf, score: 52.137	benign	0.729	TOLERATED	0.07
vg0804028565	G -> DEL	LOC_Os08g07220.1	N	frameshift_variant	Average:27.455; most accessible tissue: Minghui63 flag leaf, score: 52.137	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0804028565	NA	2.46E-06	mr1076	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
vg0804028565	NA	3.51E-07	mr1082	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
vg0804028565	NA	3.27E-07	mr1083	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
vg0804028565	NA	2.00E-07	mr1226	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
vg0804028565	8.12E-08	8.12E-08	mr1076_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
vg0804028565	9.32E-06	1.53E-08	mr1082_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
vg0804028565	3.13E-08	2.18E-09	mr1083_2	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
vg0804028565	6.91E-07	NA	mr1085_2	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
vg0804028565	4.88E-07	NA	mr1103_2	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
vg0804028565	6.77E-07	NA	mr1104_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
vg0804028565	7.57E-06	7.57E-06	mr1145_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
vg0804028565	2.37E-07	NA	mr1155_2	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
vg0804028565	4.10E-07	1.77E-07	mr1226_2	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
vg0804028565	2.75E-06	1.77E-06	mr1408_2	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
vg0804028565	4.50E-07	NA	mr1437_2	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