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Detailed information for vg0420371360:

Variant ID: vg0420371360 (JBrowse)	Variation Type: INDEL
Chromosome: chr04	Position: 20371360
Reference Allele: CCCTT	Alternative Allele: C,TCCTT
Primary Allele: CCCTT	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GCAACCTCCTAGAAAAGGAGAAAGTCGCTGCGCCAAGAAAAGGAAAACGATGCCTGAGTCGGAGATTTGGCCTTGGAGATAAACCTGCAAATCACAGTGA[CCCTT/C,TCCTT]
ATTGAATAGCCCGTGGCACTATAGATCGCAGTCTGTGGCGTGCAACTGGATGAATTTGAACCGGACCAAATCACATGGAAGTTCATAACCCACGAGCAGT

Reverse complement sequence

ACTGCTCGTGGGTTATGAACTTCCATGTGATTTGGTCCGGTTCAAATTCATCCAGTTGCACGCCACAGACTGCGATCTATAGTGCCACGGGCTATTCAAT[AAGGG/G,AAGGA]
TCACTGTGATTTGCAGGTTTATCTCCAAGGCCAAATCTCCGACTCAGGCATCGTTTTCCTTTTCTTGGCGCAGCGACTTTCTCCTTTTCTAGGAGGTTGC

Allele Frequencies:

Populations	Population Size	Frequency of CCCTT(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	55.60%	35.30%	0.23%	0.30%	TCCTT: 8.55%
All Indica	2759	35.20%	59.00%	0.29%	0.29%	TCCTT: 5.22%
All Japonica	1512	99.30%	0.40%	0.07%	0.13%	TCCTT: 0.13%
Aus	269	10.00%	4.50%	0.37%	0.00%	TCCTT: 85.13%
Indica I	595	7.10%	92.60%	0.34%	0.00%	NA
Indica II	465	35.30%	60.00%	0.00%	0.86%	TCCTT: 3.87%
Indica III	913	51.80%	41.90%	0.55%	0.00%	TCCTT: 5.70%
Indica Intermediate	786	37.20%	52.80%	0.13%	0.51%	TCCTT: 9.41%
Temperate Japonica	767	99.60%	0.40%	0.00%	0.00%	NA
Tropical Japonica	504	99.00%	0.60%	0.00%	0.20%	TCCTT: 0.20%
Japonica Intermediate	241	98.80%	0.00%	0.41%	0.41%	TCCTT: 0.41%
VI/Aromatic	96	70.80%	1.00%	0.00%	0.00%	TCCTT: 28.12%
Intermediate	90	68.90%	23.30%	1.11%	4.44%	TCCTT: 2.22%

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0420371360	CCCTT -> TCCTT	LOC_Os04g33640.1	upstream_gene_variant ; 1553.0bp to feature; MODIFIER	silent_mutation	Average:71.033; most accessible tissue: Zhenshan97 flag leaf, score: 88.111	N	N	N	N
vg0420371360	CCCTT -> TCCTT	LOC_Os04g33640.2	upstream_gene_variant ; 1785.0bp to feature; MODIFIER	silent_mutation	Average:71.033; most accessible tissue: Zhenshan97 flag leaf, score: 88.111	N	N	N	N
vg0420371360	CCCTT -> TCCTT	LOC_Os04g33630.1	downstream_gene_variant ; 2131.0bp to feature; MODIFIER	silent_mutation	Average:71.033; most accessible tissue: Zhenshan97 flag leaf, score: 88.111	N	N	N	N
vg0420371360	CCCTT -> TCCTT	LOC_Os04g33630-LOC_Os04g33640	intergenic_region ; MODIFIER	silent_mutation	Average:71.033; most accessible tissue: Zhenshan97 flag leaf, score: 88.111	N	N	N	N
vg0420371360	CCCTT -> DEL	N	N	silent_mutation	Average:71.033; most accessible tissue: Zhenshan97 flag leaf, score: 88.111	N	N	N	N
vg0420371360	CCCTT -> C	LOC_Os04g33640.1	upstream_gene_variant ; 1552.0bp to feature; MODIFIER	silent_mutation	Average:71.033; most accessible tissue: Zhenshan97 flag leaf, score: 88.111	N	N	N	N
vg0420371360	CCCTT -> C	LOC_Os04g33640.2	upstream_gene_variant ; 1784.0bp to feature; MODIFIER	silent_mutation	Average:71.033; most accessible tissue: Zhenshan97 flag leaf, score: 88.111	N	N	N	N
vg0420371360	CCCTT -> C	LOC_Os04g33630.1	downstream_gene_variant ; 2132.0bp to feature; MODIFIER	silent_mutation	Average:71.033; most accessible tissue: Zhenshan97 flag leaf, score: 88.111	N	N	N	N
vg0420371360	CCCTT -> C	LOC_Os04g33630-LOC_Os04g33640	intergenic_region ; MODIFIER	silent_mutation	Average:71.033; most accessible tissue: Zhenshan97 flag leaf, score: 88.111	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0420371360	NA	3.33E-14	mr1166	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
vg0420371360	NA	2.72E-07	mr1320	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
vg0420371360	NA	1.57E-06	mr1415	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
vg0420371360	NA	7.52E-07	mr1438	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
vg0420371360	NA	5.60E-07	mr1545	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
vg0420371360	NA	1.57E-06	mr1567	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
vg0420371360	NA	2.96E-11	mr1649	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
vg0420371360	4.47E-06	NA	mr1928	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