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Detailed information for vg0522357374:

Variant ID: vg0522357374 (JBrowse)	Variation Type: INDEL
Chromosome: chr05	Position: 22357374
Reference Allele: TGG	Alternative Allele: T,CGG
Primary Allele: T	Secondary Allele: TGG

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTTAATCTAGAATTCTTTCCTATCCTACTACACGTAATGTGCAATGAGGGTTGGCTTGTTGTTTATGTTTAGTTTCATTTGTTCTTCCATATTTTGTATG[TGG/T,CGG]
TGCTTCATCCTTGTGCAATTGTGTATGTACCGGCATTCTAATGTTGGTGCTTGATTTCAGGTATCCAACTGACAGCGATAAGCAGATGCTTGCTAAACAG

Reverse complement sequence

CTGTTTAGCAAGCATCTGCTTATCGCTGTCAGTTGGATACCTGAAATCAAGCACCAACATTAGAATGCCGGTACATACACAATTGCACAAGGATGAAGCA[CCA/A,CCG]
CATACAAAATATGGAAGAACAAATGAAACTAAACATAAACAACAAGCCAACCCTCATTGCACATTACGTGTAGTAGGATAGGAAAGAATTCTAGATTAAA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of TGG(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	64.60%	34.10%	0.36%	0.30%	CGG: 0.68%
All Indica	2759	98.30%	0.90%	0.11%	0.36%	CGG: 0.33%
All Japonica	1512	1.20%	96.50%	0.79%	0.07%	CGG: 1.46%
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.20%	0.30%	0.00%	0.50%	NA
Indica II	465	98.30%	1.30%	0.00%	0.22%	CGG: 0.22%
Indica III	913	99.30%	0.40%	0.00%	0.11%	CGG: 0.11%
Indica Intermediate	786	96.40%	1.70%	0.38%	0.64%	CGG: 0.89%
Temperate Japonica	767	0.80%	94.90%	1.43%	0.00%	CGG: 2.87%
Tropical Japonica	504	1.20%	98.60%	0.20%	0.00%	NA
Japonica Intermediate	241	2.50%	97.10%	0.00%	0.41%	NA
VI/Aromatic	96	6.20%	93.80%	0.00%	0.00%	NA
Intermediate	90	52.20%	41.10%	2.22%	3.33%	CGG: 1.11%

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0522357374	TGG -> T	LOC_Os05g38120.1	intron_variant ; MODIFIER	silent_mutation	Average:59.667; most accessible tissue: Zhenshan97 panicle, score: 76.605	N	N	N	N
vg0522357374	TGG -> DEL	N	N	silent_mutation	Average:59.667; most accessible tissue: Zhenshan97 panicle, score: 76.605	N	N	N	N
vg0522357374	TGG -> CGG	LOC_Os05g38120.1	intron_variant ; MODIFIER	silent_mutation	Average:59.667; most accessible tissue: Zhenshan97 panicle, score: 76.605	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0522357374	NA	1.10E-07	Awn_length	Jap_All	Not	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0522357374	7.39E-07	7.39E-07	mr1008	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
vg0522357374	4.03E-06	4.03E-06	mr1009	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
vg0522357374	NA	4.39E-13	mr1035	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
vg0522357374	NA	2.62E-26	mr1072	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
vg0522357374	NA	3.60E-29	mr1075	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
vg0522357374	9.10E-06	NA	mr1124	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
vg0522357374	NA	7.17E-06	mr1140	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
vg0522357374	NA	2.76E-13	mr1149	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
vg0522357374	NA	9.33E-08	mr1162	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
vg0522357374	5.88E-06	1.79E-30	mr1202	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
vg0522357374	NA	1.98E-27	mr1238	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
vg0522357374	6.46E-06	3.42E-31	mr1309	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
vg0522357374	NA	2.59E-17	mr1484	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
vg0522357374	NA	1.25E-19	mr1541	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
vg0522357374	NA	2.41E-19	mr1566	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
vg0522357374	NA	1.15E-43	mr1591	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
vg0522357374	NA	1.41E-13	mr1592	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
vg0522357374	NA	6.55E-59	mr1594	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
vg0522357374	NA	8.36E-08	mr1613	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
vg0522357374	NA	4.48E-12	mr1626	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
vg0522357374	NA	3.66E-39	mr1645	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
vg0522357374	NA	2.54E-32	mr1647	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
vg0522357374	NA	4.05E-09	mr1663	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
vg0522357374	NA	1.11E-37	mr1719	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
vg0522357374	NA	1.56E-29	mr1737	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
vg0522357374	NA	4.50E-113	mr1750	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
vg0522357374	NA	1.98E-51	mr1795	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
vg0522357374	3.24E-07	4.38E-54	mr1861	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
vg0522357374	NA	3.13E-13	mr1874	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
vg0522357374	NA	1.39E-39	mr1890	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
vg0522357374	NA	1.51E-39	mr1891	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
vg0522357374	NA	5.48E-15	mr1900	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
vg0522357374	NA	8.95E-07	mr1962	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
vg0522357374	NA	3.01E-16	mr1416_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
vg0522357374	NA	2.82E-29	mr1631_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
vg0522357374	NA	2.34E-19	mr1900_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
vg0522357374	NA	1.18E-18	mr1945_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