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Detailed information for vg0724522889:

Variant ID: vg0724522889 (JBrowse)	Variation Type: INDEL
Chromosome: chr07	Position: 24522889
Reference Allele: GGGAGTATTAGAC	Alternative Allele: AGGAGTATTAGAC,G
Primary Allele: GGGAGTATTAGAC	Secondary Allele: AGGAGTATTAGAC

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GAAACTCCGAAAATTACAGTCTTGGCCTCCAACGGCTAGTTTTTGAGGGGCTCGGGTATATAAACTCCTCCACCCCTCCTTTGAGTTGCTGCTGCTCTTG[GGGAGTATTAGAC/AGGAGTATTAGAC,G]
ACATCCAAAGCCAAATAGCATCCCCATTTCCCTACCTTTGTGGTGCCTCTTTGTGAGGGGGATTTGAGAAGGGGAGAGAGTTGGATTGAGAGAGTGAGGA

Reverse complement sequence

TCCTCACTCTCTCAATCCAACTCTCTCCCCTTCTCAAATCCCCCTCACAAAGAGGCACCACAAAGGTAGGGAAATGGGGATGCTATTTGGCTTTGGATGT[GTCTAATACTCCC/GTCTAATACTCCT,C]
CAAGAGCAGCAGCAACTCAAAGGAGGGGTGGAGGAGTTTATATACCCGAGCCCCTCAAAAACTAGCCGTTGGAGGCCAAGACTGTAATTTTCGGAGTTTC

Allele Frequencies:

Populations	Population Size	Frequency of GGGAGTATTAGAC(primary allele)	Frequency of AGGAGTATTAGAC(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	78.90%	9.50%	6.54%	5.06%	G: 0.04%
All Indica	2759	84.70%	9.30%	5.69%	0.22%	G: 0.07%
All Japonica	1512	83.50%	0.50%	1.46%	14.55%	NA
Aus	269	15.60%	47.60%	36.80%	0.00%	NA
Indica I	595	70.40%	14.50%	15.13%	0.00%	NA
Indica II	465	92.30%	4.50%	2.15%	1.08%	NA
Indica III	913	89.00%	9.30%	1.53%	0.00%	G: 0.11%
Indica Intermediate	786	86.10%	8.10%	5.47%	0.13%	G: 0.13%
Temperate Japonica	767	71.80%	0.40%	2.09%	25.68%	NA
Tropical Japonica	504	97.60%	0.00%	0.20%	2.18%	NA
Japonica Intermediate	241	90.90%	2.10%	2.07%	4.98%	NA
VI/Aromatic	96	18.80%	49.00%	22.92%	9.38%	NA
Intermediate	90	75.60%	10.00%	10.00%	4.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0724522889	GGGAGTATTAGAC -> DEL	N	N	silent_mutation	Average:8.3; most accessible tissue: Minghui63 root, score: 21.615	N	N	N	N
vg0724522889	GGGAGTATTAGAC -> AGGAGTATTAGAC	LOC_Os07g40986.1	intron_variant ; MODIFIER	silent_mutation	Average:8.3; most accessible tissue: Minghui63 root, score: 21.615	N	N	N	N
vg0724522889	GGGAGTATTAGAC -> AGGAGTATTAGAC	LOC_Os07g40986.2	intron_variant ; MODIFIER	silent_mutation	Average:8.3; most accessible tissue: Minghui63 root, score: 21.615	N	N	N	N
vg0724522889	GGGAGTATTAGAC -> G	LOC_Os07g40986.1	intron_variant ; MODIFIER	silent_mutation	Average:8.3; most accessible tissue: Minghui63 root, score: 21.615	N	N	N	N
vg0724522889	GGGAGTATTAGAC -> G	LOC_Os07g40986.2	intron_variant ; MODIFIER	silent_mutation	Average:8.3; most accessible tissue: Minghui63 root, score: 21.615	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0724522889	2.00E-09	7.30E-12	mr1138	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
vg0724522889	1.12E-12	1.12E-12	mr1343	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
vg0724522889	7.68E-09	2.15E-08	mr1354	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
vg0724522889	1.44E-20	1.88E-26	mr1354	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
vg0724522889	4.58E-11	2.43E-16	mr1829	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
vg0724522889	5.07E-11	5.73E-14	mr1902	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
vg0724522889	4.59E-08	6.41E-10	mr1138_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
vg0724522889	9.12E-08	9.12E-08	mr1181_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
vg0724522889	5.28E-11	1.67E-11	mr1354_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
vg0724522889	1.66E-23	5.37E-31	mr1354_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
vg0724522889	NA	3.04E-07	mr1567_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
vg0724522889	2.59E-08	2.97E-11	mr1567_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
vg0724522889	NA	2.53E-06	mr1621_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
vg0724522889	2.53E-06	3.16E-08	mr1679_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
vg0724522889	9.29E-07	NA	mr1699_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
vg0724522889	7.08E-06	7.08E-06	mr1714_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
vg0724522889	2.69E-08	NA	mr1829_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
vg0724522889	4.08E-13	1.63E-23	mr1829_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
vg0724522889	2.57E-08	NA	mr1902_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
vg0724522889	1.95E-13	5.65E-24	mr1902_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