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Detailed information for vg1001167572:

Variant ID: vg1001167572 (JBrowse)	Variation Type: INDEL
Chromosome: chr10	Position: 1167572
Reference Allele: TGTTGATGTGATGGAAAAAATTGGAAGTTTGGATCTAAACACACAGCCTCAGTTGGGTTCTC	Alternative Allele: GGTTGATGTGATGGAAAAAATTGGAAGTTTGGATCTAAACACACAGCCTCAGTTGGGTTCTC,T
Primary Allele: GGTTGATGTGATGGAAAAAA TTGGAAGTTTGGATCTAAAC ACACAGCCTCAGTTGGGTTC TC	Secondary Allele: TGTTGATGTGATGGAAAAAA TTGGAAGTTTGGATCTAAAC ACACAGCCTCAGTTGGGTTC TC

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AAAACTTAATCTCACCTCAGGTTGTGTTTAGTTCCTTCCAAACTTAGAAGTTTGGGTTGAAATTGATACGATGTGACTGAAAAGTTGTGTGTGTATGACA[TGTTGATGTGATGGAAAAAATTGGAAGTTTGGATCTAAACACACAGCCTCAGTTGGGTTCTC/GGTTGATGTGATGGAAAAAATTGGAAGTTTGGATCTAAACACACAGCCTCAGTTGGGTTCTC,T]
GAACAGGACCTTATTCAGTGTTCGTTCGCGGCCTCATTCTGGTGCTCCATGGAAATTCAGCTCAATACCATAAGTGCCAAAGACCTGGCAAGGCTGGTTG

Reverse complement sequence

CAACCAGCCTTGCCAGGTCTTTGGCACTTATGGTATTGAGCTGAATTTCCATGGAGCACCAGAATGAGGCCGCGAACGAACACTGAATAAGGTCCTGTTC[GAGAACCCAACTGAGGCTGTGTGTTTAGATCCAAACTTCCAATTTTTTCCATCACATCAACA/GAGAACCCAACTGAGGCTGTGTGTTTAGATCCAAACTTCCAATTTTTTCCATCACATCAACC,A]
TGTCATACACACACAACTTTTCAGTCACATCGTATCAATTTCAACCCAAACTTCTAAGTTTGGAAGGAACTAAACACAACCTGAGGTGAGATTAAGTTTT

Allele Frequencies:

Populations	Population Size	Frequency of GGTTGATGTGATGGAAAAAA TTGGAAGTTTGGATCTAAAC ACACAGCCTCAGTTGGGTTC TC(primary allele)	Frequency of TGTTGATGTGATGGAAAAAA TTGGAAGTTTGGATCTAAAC ACACAGCCTCAGTTGGGTTC TC(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	60.00%	17.60%	2.67%	19.66%	T: 0.08%
All Indica	2759	56.50%	7.40%	4.39%	31.71%	NA
All Japonica	1512	56.70%	40.00%	0.07%	3.24%	NA
Aus	269	95.20%	1.90%	1.12%	0.37%	T: 1.49%
Indica I	595	47.10%	3.00%	4.54%	45.38%	NA
Indica II	465	70.50%	3.00%	3.23%	23.23%	NA
Indica III	913	54.90%	13.40%	3.83%	27.93%	NA
Indica Intermediate	786	57.30%	6.40%	5.60%	30.79%	NA
Temperate Japonica	767	28.40%	71.30%	0.00%	0.26%	NA
Tropical Japonica	504	88.30%	2.60%	0.00%	9.13%	NA
Japonica Intermediate	241	80.50%	18.70%	0.41%	0.41%	NA
VI/Aromatic	96	95.80%	4.20%	0.00%	0.00%	NA
Intermediate	90	77.80%	16.70%	1.11%	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
vg1001167572	TGTTGATGTGATGGAAAAAATTGGAAGTTTGGATCTAAACACACAGCCTCAGTTGGGTTCTC -> GGTTGATGTGATGGAAAAAATTGGAAGTTT GGATCTAAACACACAGCCTCAGTTGGGTTC TC	LOC_Os10g02880.1	upstream_gene_variant ; 3087.0bp to feature; MODIFIER	silent_mutation	Average:55.196; most accessible tissue: Zhenshan97 flower, score: 79.53	N	N	N	N
vg1001167572	TGTTGATGTGATGGAAAAAATTGGAAGTTTGGATCTAAACACACAGCCTCAGTTGGGTTCTC -> GGTTGATGTGATGGAAAAAATTGGAAGTTT GGATCTAAACACACAGCCTCAGTTGGGTTC TC	LOC_Os10g02880-LOC_Os10g02890	intergenic_region ; MODIFIER	silent_mutation	Average:55.196; most accessible tissue: Zhenshan97 flower, score: 79.53	N	N	N	N
vg1001167572	TGTTGATGTGATGGAAAAAATTGGAAGTTTGGATCTAAACACACAGCCTCAGTTGGGTTCTC -> T	LOC_Os10g02880.1	upstream_gene_variant ; 3088.0bp to feature; MODIFIER	silent_mutation	Average:55.196; most accessible tissue: Zhenshan97 flower, score: 79.53	N	N	N	N
vg1001167572	TGTTGATGTGATGGAAAAAATTGGAAGTTTGGATCTAAACACACAGCCTCAGTTGGGTTCTC -> T	LOC_Os10g02880-LOC_Os10g02890	intergenic_region ; MODIFIER	silent_mutation	Average:55.196; most accessible tissue: Zhenshan97 flower, score: 79.53	N	N	N	N
vg1001167572	TGTTGATGTGATGGAAAAAATTGGAAGTTTGGATCTAAACACACAGCCTCAGTTGGGTTCTC -> DEL	N	N	silent_mutation	Average:55.196; most accessible tissue: Zhenshan97 flower, score: 79.53	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1001167572	NA	4.01E-06	mr1010	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
vg1001167572	NA	5.08E-06	mr1192	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
vg1001167572	NA	2.03E-08	mr1206	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
vg1001167572	NA	7.32E-06	mr1236	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
vg1001167572	NA	6.44E-06	mr1328	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
vg1001167572	NA	3.26E-06	mr1330	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
vg1001167572	NA	6.41E-37	mr1486	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
vg1001167572	NA	5.21E-12	mr1486	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
vg1001167572	NA	9.09E-07	mr1521	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
vg1001167572	NA	2.16E-07	mr1548	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
vg1001167572	NA	7.86E-09	mr1570	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
vg1001167572	NA	2.60E-08	mr1617	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
vg1001167572	NA	1.57E-08	mr1627	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
vg1001167572	NA	1.04E-07	mr1715	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
vg1001167572	NA	1.27E-08	mr1825	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
vg1001167572	NA	1.77E-22	mr1920	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
vg1001167572	7.78E-06	NA	mr1926	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
vg1001167572	4.43E-07	NA	mr1932	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
vg1001167572	NA	5.10E-06	mr1937	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
vg1001167572	NA	2.59E-10	mr1959	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
vg1001167572	NA	9.39E-07	mr1161_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
vg1001167572	NA	2.36E-33	mr1310_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
vg1001167572	1.46E-06	NA	mr1486_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
vg1001167572	NA	3.02E-12	mr1486_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
vg1001167572	NA	9.34E-08	mr1570_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
vg1001167572	NA	8.99E-06	mr1617_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
vg1001167572	NA	3.96E-14	mr1959_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