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Medium Indels (Koboldt et al. BMC Genomics 2010)

Table 3 from the paper (DOI: 10.1186/1471-2164-11-236)

ChrIndel IDLocation (cM)Ultra_contigAF16 amplicon (bp) predictedAF16 amplicon (bp) observedHK104 amplicon (bp) predictedHK104 amplicon (bp) observedPredicted indelValidation statusValidation type
1cb-m14212.6cb25.fpc4321665700915950250 bp insertion250 bp insertion*
cb-m213.4cb25.fpc43211461Failed PCR1125Failed PCR336 bp deletionFailed PCR
cb-m520.0cb25.fpc4171774750674Failed PCR100 bp deletionFailed PCR
cb-m520.0cb25.fpc4171461500361500100 bp deletionno indel
cb-m643.9cb25.fpc41409309007851000145 bp deletion100 bp insertion**
cb-m13unknowncb25.fpc0078504420385400119 bp deletion20 bp deletion**
cb-m14unknowncb25.fpc412710001000676710324 bp deletion290 bp deletion*
cb-m146unknowncb25.fpc4122406480506530100 bp insertion50 bp insertion**
cb-m12unknowncb25.fpc4127921Failed PCR4161000505 bp deletionFailed PCR
2cb-m2124.2cb25.fpc0058825900670700155 bp deletion200 bp deletion*
cb-m1637.4cb25.fpc40711097>1500687>1500410 bp deletionunclear
cb-m1911.9-13.1cb25.fpc001113641013828750536 bp deletion263 bp deletion**
cb-m14927.9-34.0cb25.fpc4206470490603600133 bp insertion110 bp insertion*
cb-m2627.9-34.0cb25.fpc4206678700407410271 bp deletion290 bp deletion*
cb-m38unknowncb25.fpc4131835860544600291 bp deletion260 bp deletion*
bdP4unknowncb25.fpc24411013~990903~880110 bp deletion110 bp deletion*
3cb-m466.1cb25.fpc25877471020574750173 bp deletion270 bp deletion*
cb-m1556.1cb25.fpc25871169Failed PCR1329Failed PCR160 bp insertionFailed PCR
cb-m4821.2cb25.fpc2976116312006441200519 bp deletionno indel
cb-m20525.8cb25.fpc40796717009711000300 bp insertion300 bp insertion*
cb-m15936.5cb25.fpc4224463500655Failed PCR192 bp insertionFailed PCR
cb-m16028.8-29.3cb25.fpc2193821100010531200232 bp insertion200 bp insertion*
bdP131.3cb25.fpc00021723~1700~1500~1500~200 bp deletion200 bp deletion*
4cb-m17218.2cb25.fpc0039650700904950254 bp insertion250 bp insertion*
cb-m17020.6cb25.fpc4090691720931Failed PCR240 bp insertionFailed PCR
cb-m17125.5cb25.fpc413238145047655095 bp insertion100 bp insertion*
cb-m7025.5cb25.fpc4132594>16004211600173 bp deletionvery large indel**
cb-m17637.5-41.2cb25.fpc3835732Failed PCR1014Failed PCR282 bp insertionFailed PCR
cb-m7437.5-41.2cb25.fpc38356771000523700154 bp deletion300 bp deletion**
cb-m7642.4-43.0cb25.fpc2328709900527550182 bp deletion350 bp deletion**
cb-m1779.2-9.8cb25.fpc4118801800946900145 bp insertion100 bp insertion*
cb-m179unknowncb25.fpc4331383450500520117 bp insertion70 bp insertion*
5cb-m10319.0cb25.fpc2220600700454500146 bp deletion200 bp deletion*
cb-m9746.1cb25.fpc4109591705392490199 bp deletion215 bp deletion*
cb-m10537.0-37.7cb25.fpc4063692800454520238 bp deletion280 bp deletion*
cb-m10437.0-37.7cb25.fpc4063942Failed PCR661Failed PCR281 bp deletionFailed PCR
Xcb-m1973.5cb25.fpc4033692700855790163 bp insertion90 bp insertion*
cb-m20417.4cb25.fpc40446897509491000260 bp insertion250 bp insertion*
cb-m13630.1cb25.fpc082914402000645750795 bp deletion1250 bp deletion*
cb-m12734.1cb25.fpc2334486600349405137 bp deletion195 bp deletion*
cb-m12634.1cb25.fpc2334785Failed PCR648Failed PCR137 bp deletionFailed PCR
cb-m13527.4-34.1cb25.fpc0829720900584Failed PCR136 bp deletionFailed PCR
The indels are arranged by chromosome and location. The corresponding ultracontigs are also listed. The “unknown” locations refer to unassembled contigs. The predicted indel sizes are based on in silico analysis of AF16 and HK104 amplicons. The validation type column marks indels that were consistent with prediction (*) and those that differed significantly (**).