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Detailed information for vg0623040717:

Variant ID: vg0623040717 (JBrowse)	Variation Type: INDEL
Chromosome: chr06	Position: 23040717
Reference Allele: CCAGCTAGCTTCTCAG	Alternative Allele: GCAGCTAGCTTCTCAG,C
Primary Allele: CCAGCTAGCTTCTCAG	Secondary Allele: GCAGCTAGCTTCTCAG

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGTCCAGCTTTTTACCCAGATTCTGAGAATCTGTAGTTGTAGAATCTGAAAAATGAACTAGAAGCCAGAAGCTGGGTTTTCCAGCTTCTCCAGATTCTCA[CCAGCTAGCTTCTCAG/GCAGCTAGCTTCTCAG,C]
CAGCTGCTTCTCAAAATCTTAAGCTCCCCCCAAACAGGCCCTATCTTAAGCTTCTCAGCATTGTAGCGTGGGTGTGGTCCAGATTTGTTGAGCGAGATAT

Reverse complement sequence

ATATCTCGCTCAACAAATCTGGACCACACCCACGCTACAATGCTGAGAAGCTTAAGATAGGGCCTGTTTGGGGGGAGCTTAAGATTTTGAGAAGCAGCTG[CTGAGAAGCTAGCTGG/CTGAGAAGCTAGCTGC,G]
TGAGAATCTGGAGAAGCTGGAAAACCCAGCTTCTGGCTTCTAGTTCATTTTTCAGATTCTACAACTACAGATTCTCAGAATCTGGGTAAAAAGCTGGACT

Allele Frequencies:

Populations	Population Size	Frequency of CCAGCTAGCTTCTCAG(primary allele)	Frequency of GCAGCTAGCTTCTCAG(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	75.30%	7.20%	0.93%	16.59%	C: 0.04%
All Indica	2759	82.60%	0.40%	0.29%	16.64%	C: 0.07%
All Japonica	1512	67.00%	21.00%	1.12%	10.85%	NA
Aus	269	43.90%	0.00%	1.12%	55.02%	NA
Indica I	595	97.60%	0.00%	0.17%	1.85%	C: 0.34%
Indica II	465	86.70%	1.70%	0.22%	11.40%	NA
Indica III	913	70.60%	0.10%	0.33%	28.92%	NA
Indica Intermediate	786	82.80%	0.10%	0.38%	16.67%	NA
Temperate Japonica	767	79.70%	4.20%	0.78%	15.38%	NA
Tropical Japonica	504	43.70%	50.40%	0.60%	5.36%	NA
Japonica Intermediate	241	75.50%	13.30%	3.32%	7.88%	NA
VI/Aromatic	96	76.00%	1.00%	15.62%	7.29%	NA
Intermediate	90	82.20%	10.00%	1.11%	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
vg0623040717	CCAGCTAGCTTCTCAG -> C	LOC_Os06g38820.1	upstream_gene_variant ; 3494.0bp to feature; MODIFIER	silent_mutation	Average:67.043; most accessible tissue: Zhenshan97 root, score: 78.34	N	N	N	N
vg0623040717	CCAGCTAGCTTCTCAG -> C	LOC_Os06g38810.1	intron_variant ; MODIFIER	silent_mutation	Average:67.043; most accessible tissue: Zhenshan97 root, score: 78.34	N	N	N	N
vg0623040717	CCAGCTAGCTTCTCAG -> GCAGCTAGCTTCTCAG	LOC_Os06g38820.1	upstream_gene_variant ; 3495.0bp to feature; MODIFIER	silent_mutation	Average:67.043; most accessible tissue: Zhenshan97 root, score: 78.34	N	N	N	N
vg0623040717	CCAGCTAGCTTCTCAG -> GCAGCTAGCTTCTCAG	LOC_Os06g38810.1	intron_variant ; MODIFIER	silent_mutation	Average:67.043; most accessible tissue: Zhenshan97 root, score: 78.34	N	N	N	N
vg0623040717	CCAGCTAGCTTCTCAG -> DEL	N	N	silent_mutation	Average:67.043; most accessible tissue: Zhenshan97 root, score: 78.34	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0623040717	NA	3.09E-06	mr1408	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
vg0623040717	NA	1.23E-09	mr1539	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
vg0623040717	NA	3.70E-06	mr1039_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
vg0623040717	4.04E-06	NA	mr1082_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
vg0623040717	4.16E-07	NA	mr1083_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
vg0623040717	3.33E-06	NA	mr1104_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
vg0623040717	1.04E-06	NA	mr1107_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
vg0623040717	7.21E-09	NA	mr1136_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
vg0623040717	4.41E-06	NA	mr1145_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
vg0623040717	1.66E-06	NA	mr1226_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
vg0623040717	4.09E-08	7.06E-14	mr1408_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
vg0623040717	NA	9.93E-06	mr1498_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
vg0623040717	NA	3.61E-07	mr1632_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
vg0623040717	NA	1.37E-07	mr1730_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
vg0623040717	NA	5.90E-06	mr1866_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