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["Supplemental Table S1"]
[]
["Genotypes of the 90 candidate template switch events detected between two humans. The genotypes were determined by manual inspection of the alignment files for HuRef (Li and Durbin, 2011) and for the 1000 Genomes project (The 1000 Genomes Project Consortium, 2015) reference individual (NA12878). The table columns are: position, genotypes, 1KG variation data and Ensembl annotation. For 1KG, `complete' and `incomplete' indicate if all positions affected by the template switch event are explained; `two events' and `different' indicate cases where the mutation pattern is created by two separate events or where the different data sets contain distinct events."]
[]
["Position (GRCh37)","HuRef","NA12878","1KG","mutations","DAF","Ensembl consequence"]
["chr1:8583720-8583736 ","variant ","heterozygote ","incomplete ","1 SNP, 1 indel ",0.65,"intron_variant  "]
["chr1:58225718-58225744 ","heterozygote ","variant ","complete ","5 SNPs ",0.13,"intron_variant  "]
["chr1:68552103-68552132 ","heterozygote ","heterozygote ","complete ","7 SNPs, 4 indels",0.43,"intron_variant  "]
["chr1:154541522-154541545 ","heterozygote ","reference ","- ","- ","- ","-  "]
["chr1:165419825-165419848 ","unclear ","reference ","- ","- ","- ","-  "]
["chr1:177614385-177614422 ","variant ","variant ","incomplete ","1 indel ",0.83,"intergenic_variant  "]
["chr1:194728601-194728642 ","heterozygote ","reference ","- ","- ","- ","-  "]
["chr1:248817975-248818001 ","heterozygote ","heterozygote ","- ","- ","- ","upstream_gene_variant  "]
["chr2:44545734-44545772 ","heterozygote ","variant ","incomplete ","7 SNPs, 3 indels ",0.67,"3_prime_UTR_variant  "]
["chr2:87072742-87072759 ","unclear ","reference ","- ","- ","- ","-  "]
["chr2:113399116-113399133 ","heterozygote ","variant ","complete ","2 SNPs ",0.81,"upstream_gene_variant  "]
["chr2:141481114-141481130 ","heterozygote ","variant ","complete ","2 SNPs, 1 indel ",0.84,"intron_variant  "]
["chr2:147332910-147332928 ","heterozygote ","reference ","- ","- ","- ","-  "]
["chr2:177656645-177656662 ","variant ","reference ","complete ","4 SNPs ",0.26,"intron_variant  "]
["chr2:192808311-192808331 ","variant ","variant ","complete ","3 SNPs, 1 indel ",0.93,"intron_variant  "]
["chr2:236077394-236077409 ","heterozygote ","heterozygote ","complete ","2 SNPs ",0.36,"intergenic_variant  "]
["chr3:28029612-28029627 ","heterozygote ","reference ","- ","- ","- ","-  "]
["chr3:79662007-79662071 ","unclear ","reference ","- ","- ","- ","-  "]
["chr3:85078066-85078133 ","variant ","variant ","incomplete ","2 indels ",0.7,"intron_variant   "]
["chr3:99913203-99913218 ","heterozygote ","reference ","- ","- ","- ","-  "]
["chr3:107924354-107924379 ","unclear ","reference ","- ","- ","- ","-  "]
["chr3:163871744-163871758 ","heterozygote ","reference ","complete ","1 SNP, 1 indel ",0.55,"intergenic_variant  "]
["chr3:170821849-170821880 ","variant ","variant ","incomplete ","1 SNP, 4 indels ",0.98,"intron_variant  "]
["chr4:43027132-43027152 ","variant ","reference ","complete ","3 SNPs ",0.87,"intron_variant  "]
["chr4:54752568-54752582 ","variant ","variant ","incomplete ","2 indels ",0.77,"intron_variant  "]
["chr4:56980429-56980450 ","unclear ","reference ","- ","- ","- ","-  "]
["chr4:67591134-67591154 ","heterozygote ","reference ","- ","- ","- ","-  "]
["chr4:84454349-84454369 ","heterozygote ","reference ","- ","- ","- ","-  "]
["chr4:120423355-120423371 ","heterozygote ","reference ","- ","- ","- ","-  "]
["chr4:142875495-142875523 ","heterozygote ","reference ","- ","- ","- ","-  "]
["chr4:175312410-175312423 ","heterozygote ","reference ","incomplete ","1 indel ",0.23,"intergenic_variant  "]
["chr4:182127597-182127623 ","variant ","variant ","incomplete ","1 SNP ",0.999,"intergenic_variant  "]
["chr5:41047165-41047178 ","variant ","variant ","complete ","3 SNPs, 1 indel ",0.76,"intron_variant  "]
["chr5:69245706-69245719 ","unclear ","reference ","- ","- ","- ","-  "]
["chr5:70120774-70120787 ","unclear ","reference ","- ","- ","- ","-  "]
["chr5:107452444-107452460 ","variant ","variant ","complete ","1 SNP, 1 indel ",0.7,"intron_variant  "]
["chr5:120770300-120770325 ","variant ","variant ","complete ","2 SNPs ",0.92,"intergenic_variant  "]
["chr6:3027013-3027033 ","heterozygote ","variant ","complete ","2 SNPs, 2 indels ",0.65,"non_coding_transcript_exon_variant "]
["chr6:4365709-4365735 ","variant ","variant ","incomplete ","7 SNPs, 1 indel ",0.999,"intergenic_variant  "]
["chr6:44403373-44403386 ","heterozygote ","reference ","- ","- ","- ","-  "]
["chr6:105308170-105308190 ","variant ","variant ","complete ","3 SNPs ",0.998,"upstream_gene_variant  "]
["chr6:128673556-128673569 ","variant ","variant ","incomplete ","2 indels ",0.97,"intron_variant  "]
["chr6:129988189-129988211 ","variant ","heterozygote ","complete ","3 SNPs ",0.51,"intron_variant  "]
["chr6:151077057-151077091 ","heterozygote ","heterozygote ","complete ","6 SNPs, 2 indels ",0.19,"intron_variant  "]
["chr7:9995542-9995576 ","heterozygote ","variant ","complete ","17 SNPs ",0.34,"intergenic_variant  "]
["chr7:117357034-117357068 ","variant ","variant ","- ","- ","- ","intron_variant  "]
["chr7:118367022-118367036 ","heterozygote ","reference ","incomplete ","4 SNPs ",0.21,"intergenic_variant  "]
["chr8:3212293-3212315 ","variant/heteroz. ","heteroz./refer. ","two events ","1 SNP/1 indel ","0.44/0.07 ","intron_variant  "]
["chr8:78174872-78174903 ","heterozygote ","variant ","complete ","4 SNPs ",0.89,"intergenic_variant  "]
["chr8:139290452-139290493 ","variant ","variant ","complete ","3 SNPs ",1,"intron_variant  "]
["chr9:13322919-13322940 ","unclear ","reference ","- ","- ","- ","-  "]
["chr9:73792526-73792553 ","variant ","variant ","incomplete ","2 SNPs, 1 indel",0.42,"intron_variant  "]
["chr9:87283156-87283169 ","variant ","reference ","complete ","2 SNPs ",0.75,"upstream_gene_variant  "]
["chr9:122667309-122667335 ","heterozygote ","variant ","complete ","2 SNPs, 1 indel ",0.51,"intergenic_variant  "]
["chr9:139101513-139101536 ","heterozygote ","reference ","- ","- ","- ","-  "]
["chr10:3173066-3173095 ","variant ","reference ","complete ","11 SNPs, 2 indels",0.28,"intron_variant  "]
["chr10:29421801-29421866 ","heterozygote ","reference ","incomplete ","19 SNPs ",0.35,"intergenic_variant  "]
["chr10:30227468-30227486 ","variant ","reference ","- ","- ","- ","intergenic_variant  "]
["chr10:46341630-46341643 ","unclear ","reference ","- ","- ","- ","-  "]
["chr10:51245239-51245257 ","unclear ","unclear ","- ","- ","- ","-  "]
["chr10:51987097-51987112 ","unclear ","unclear ","- ","- ","- ","-  "]
["chr10:72001951-72001968 ","variant ","variant ","complete ","2 SNPs ",0.87,"intergenic_variant  "]
["chr11:63682312-63682327 ","variant ","variant ","different ","3 SNPs; 1 SNP, 1 indel",0.86,"intron_variant"]
["chr11:73442141-73442164 ","variant ","variant ","complete ","4 SNPs ",0.93,"intron_variant  "]
["chr11:109759306-109759342 ","unclear ","reference ","- ","- ","- ","-  "]
["chr12:115753415-115753430 ","heterozygote ","heterozygote ","different ","- ","- ","intergenic_variant  "]
["chr12:130252986-130253045 ","variant ","variant ","complete ","3 SNPs ","0.84-0.95 ","intron_variant  "]
["chr12:133652922-133652951 ","heterozygote ","variant ","- ","- ","- ","upstream_gene_variant  "]
["chr13:113111734-113111749 ","variant ","variant ","incomplete ","1 SNP, 2 indels ",0.9,"intergenic_variant  "]
["chr14:31692897-31692925 ","variant ","variant ","complete ","3 SNPs ",0.99]
["chr14:39602394-39602418 ","variant/heteroz. ","variant/refer. ","two events ","1 SNP/1 indel ","0.80/0.18 ","intron_variant  "]
["chr14:42277232-42277262 ","heterozygote ","reference ","- ","- ","- ","-  "]
["chr15:36259779-36259809 ","variant ","heterozygote ","complete ","7 SNPs, 2 indels ",0.06,"intron_variant  "]
["chr15:65337095-65337109 ","heterozygote ","reference ","- ","- ","- ","-  "]
["chr15:70584124-70584137 ","heterozygote ","reference ","- ","- ","- ","-  "]
["chr15:72960868-72960885 ","unclear ","reference ","- ","- ","- ","-  "]
["chr15:78427835-78427877 ","heterozygote ","reference ","- ","- ","- ","-  "]
["chr16:12708977-12709007 ","heterozygote ","reference ","complete ","3 SNPs ",0.57,"upstream_gene_variant  "]
["chr16:84986430-84986443 ","unclear ","reference ","- ","- ","- ","-  "]
["chr17:33622098-33622114 ","variant ","reference ","complete ","2 SNPs, 3 indels ",0.39,"intergenic_variant  "]
["chr17:59744593-59744623 ","heterozygote ","variant ","incomplete ","2 SNPs ",0.56,"intergenic_variant  "]
["chr18:69556840-69556858 ","variant ","variant ","complete ","2 SNPs ",0.99,"downstream_gene_variant  "]
["chr19:767508-767527 ","heterozygote ","variant ","complete ","2 SNPs ",0.8,"downstream_gene_variant  "]
["chr19:38062901-38062937 ","heterozygote ","variant ","complete ","4 SNPs, 6 indels ",0.81,"intron_variant  "]
["chr21:16013327-16013340 ","heterozygote ","variant ","complete ","3 SNPs, 2 indels ",0.74,"intron_variant  "]
["chr22:18938180-18938203 ","heterozygote ","heterozygote ","complete ","2 SNPs ",0.2,"intergenic_variant  "]
["chr22:42751380-42751399 ","heterozygote ","reference ","- ","- ","- ","-  "]
["chr22:46457691-46457720 ","variant ","reference ","complete ","4 SNPs ",0.003,"intron_variant  "]
["chrX:35587707-35587736 ","variant ","reference ","- ","- ","- ","-  "]
["chrX:69286974-69286995 ","variant ","variant ","incomplete ","3 SNPs ",0.9,"downstream_gene_variant  "]